diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 5b705a647..4407ee5b3 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -27,7 +27,7 @@ jobs: steps: - name: Add reaction if: ${{ github.event.client_payload.slash_command.command == 'run-all-workflow-tests' }} - uses: peter-evans/create-or-update-comment@v2 + uses: peter-evans/create-or-update-comment@v4 with: token: ${{ secrets.PAT }} repository: ${{ github.event.client_payload.github.payload.repository.full_name }} @@ -43,11 +43,11 @@ jobs: - name: Determine latest commit in the Galaxy repo id: get-galaxy-sha run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ steps.get-fork-branch.outputs.fork }}/galaxy refs/heads/${{ steps.get-fork-branch.outputs.branch }} | cut -f1)" >> $GITHUB_OUTPUT - - uses: actions/setup-python@v4 + - uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Cache .cache/pip - uses: actions/cache@v3 + uses: actions/cache@v4 id: cache-pip with: path: ~/.cache/pip @@ -56,7 +56,7 @@ jobs: # are not available as wheels, pip will build a wheel for them, which can be cached. - name: Install wheel run: pip install wheel - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: fetch-depth: 1 - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks @@ -85,14 +85,14 @@ jobs: matrix: python-version: ['3.11'] steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: fetch-depth: 1 - - uses: actions/setup-python@v4 + - uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Cache .cache/pip - uses: actions/cache@v3 + uses: actions/cache@v4 id: cache-pip with: path: ~/.cache/pip @@ -105,6 +105,7 @@ jobs: mode: lint workflows: true repository-list: "${{ needs.setup.outputs.repository-list }}" + additional-planemo-options: --iwc test: name: Test workflows @@ -129,14 +130,14 @@ jobs: steps: # checkout the repository # and use it as the current working directory - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: fetch-depth: 1 - - uses: actions/setup-python@v4 + - uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Cache .cache/pip - uses: actions/cache@v3 + uses: actions/cache@v4 id: cache-pip with: path: ~/.cache/pip @@ -153,7 +154,7 @@ jobs: galaxy-branch: ${{ needs.setup.outputs.branch }} chunk: ${{ matrix.chunk }} chunk-count: ${{ needs.setup.outputs.chunk-count }} - - uses: actions/upload-artifact@v3 + - uses: actions/upload-artifact@v4 with: name: 'Workflow test output ${{ matrix.chunk }}' path: upload @@ -172,14 +173,14 @@ jobs: # This job runs on Linux runs-on: ubuntu-latest steps: - - uses: actions/download-artifact@v3 + - uses: actions/download-artifact@v4 with: path: artifacts - - uses: actions/setup-python@v4 + - uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Cache .cache/pip - uses: actions/cache@v3 + uses: actions/cache@v4 id: cache-pip with: path: ~/.cache/pip @@ -190,7 +191,7 @@ jobs: with: mode: combine html-report: true - - uses: actions/upload-artifact@v3 + - uses: actions/upload-artifact@v4 with: name: 'All workflow test results' path: upload @@ -201,7 +202,7 @@ jobs: - name: Create comment if: ${{ github.event.client_payload.slash_command.command == 'run-all-workflow-tests' }} - uses: peter-evans/create-or-update-comment@v2 + uses: peter-evans/create-or-update-comment@v4 with: token: ${{ secrets.PAT }} repository: ${{ github.event.client_payload.github.payload.repository.full_name }} diff --git a/.github/workflows/enable_ci_workflows.yml b/.github/workflows/enable_ci_workflows.yml index b7a1999c7..875dfe950 100644 --- a/.github/workflows/enable_ci_workflows.yml +++ b/.github/workflows/enable_ci_workflows.yml @@ -8,7 +8,7 @@ jobs: name: Enable CI workflows runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: fetch-depth: 1 - name: run Python script diff --git a/.github/workflows/setup.yml b/.github/workflows/setup.yml index 3b0968249..d27bb5919 100644 --- a/.github/workflows/setup.yml +++ b/.github/workflows/setup.yml @@ -60,17 +60,17 @@ jobs: - name: Determine latest commit in the Galaxy repo id: get-galaxy-sha run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ inputs.galaxy-fork }}/galaxy refs/heads/${{ inputs.galaxy-branch }} | cut -f1)" >> $GITHUB_OUTPUT - - uses: actions/setup-python@v4 + - uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Cache .cache/pip - uses: actions/cache@v3 + uses: actions/cache@v4 id: cache-pip with: path: ~/.cache/pip key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }} - name: Cache .planemo - uses: actions/cache@v3 + uses: actions/cache@v4 id: cache-planemo with: path: ~/.planemo @@ -79,7 +79,7 @@ jobs: # are not available as wheels, pip will build a wheel for them, which can be cached. - name: Install wheel run: pip install wheel - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: fetch-depth: 0 - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks diff --git a/.github/workflows/slash.yaml b/.github/workflows/slash.yaml index 8f9e2b2fe..1ffa52169 100644 --- a/.github/workflows/slash.yaml +++ b/.github/workflows/slash.yaml @@ -8,7 +8,7 @@ jobs: steps: - name: Slash Command Dispatch if: github.repository_owner == 'galaxyproject' - uses: peter-evans/slash-command-dispatch@v3 + uses: peter-evans/slash-command-dispatch@v4 with: token: ${{ secrets.PAT }} commands: | diff --git a/.github/workflows/test_workflows.yml b/.github/workflows/test_workflows.yml index 073e37fc5..0905114ac 100644 --- a/.github/workflows/test_workflows.yml +++ b/.github/workflows/test_workflows.yml @@ -60,18 +60,20 @@ jobs: ports: - 5432:5432 steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: fetch-depth: 1 - - uses: actions/setup-python@v4 + - uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Cache .cache/pip - uses: actions/cache@v3 + uses: actions/cache@v4 id: cache-pip with: path: ~/.cache/pip key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ inputs.galaxy-head-sha }} + - name: Clean dotnet folder for space + run: rm -Rf /usr/share/dotnet - name: Planemo test workflows uses: galaxyproject/planemo-ci-action@v1 id: test-workflows @@ -84,7 +86,7 @@ jobs: galaxy-branch: ${{ inputs.galaxy-branch }} chunk: ${{ matrix.chunk }} chunk-count: ${{ inputs.chunk-count }} - - uses: actions/upload-artifact@v3 + - uses: actions/upload-artifact@v4 with: name: 'Workflow test output ${{ matrix.chunk }}' path: upload diff --git a/.github/workflows/usegalaxy-star-installation.yml b/.github/workflows/usegalaxy-star-installation.yml index d6fbf8770..ea78b5f81 100644 --- a/.github/workflows/usegalaxy-star-installation.yml +++ b/.github/workflows/usegalaxy-star-installation.yml @@ -9,9 +9,9 @@ jobs: workflow-install: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Cache downloads - uses: actions/cache@v3 + uses: actions/cache@v4 with: path: | ~/.cache/pip diff --git a/.github/workflows/workflow_test.yml b/.github/workflows/workflow_test.yml index 99918de07..28d0d0b3a 100644 --- a/.github/workflows/workflow_test.yml +++ b/.github/workflows/workflow_test.yml @@ -24,14 +24,14 @@ jobs: matrix: python-version: ['3.11'] steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: fetch-depth: 1 - - uses: actions/setup-python@v4 + - uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Cache .cache/pip - uses: actions/cache@v3 + uses: actions/cache@v4 id: cache-pip with: path: ~/.cache/pip @@ -44,6 +44,7 @@ jobs: mode: lint workflows: true repository-list: "${{ needs.setup.outputs.repository-list }}" + additional-planemo-options: --iwc test: name: Test workflows @@ -69,14 +70,14 @@ jobs: python-version: ['3.11'] runs-on: ubuntu-latest steps: - - uses: actions/download-artifact@v3 + - uses: actions/download-artifact@v4 with: path: artifacts - - uses: actions/setup-python@v4 + - uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Cache .cache/pip - uses: actions/cache@v3 + uses: actions/cache@v4 id: cache-pip with: path: ~/.cache/pip @@ -94,7 +95,7 @@ jobs: - name: Debug PR number run: | cat ./upload/NR - - uses: actions/upload-artifact@v3 + - uses: actions/upload-artifact@v4 with: name: 'All tool test results' path: upload @@ -114,14 +115,14 @@ jobs: runs-on: ubuntu-latest if: github.ref == 'refs/heads/main' && github.repository_owner == 'galaxyproject' steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: fetch-depth: 1 - - uses: actions/setup-python@v4 + - uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Cache .cache/pip - uses: actions/cache@v3 + uses: actions/cache@v4 id: cache-pip with: path: ~/.cache/pip @@ -155,12 +156,12 @@ jobs: steps: # report to the PR if deployment failed - name: Get PR object - uses: 8BitJonny/gh-get-current-pr@2.2.0 + uses: 8BitJonny/gh-get-current-pr@3.0.0 id: getpr with: sha: ${{ github.event.after }} - name: Create comment - uses: peter-evans/create-or-update-comment@v3 + uses: peter-evans/create-or-update-comment@v4 with: token: ${{ secrets.PAT }} issue-number: ${{ steps.getpr.outputs.number }} diff --git a/.gitignore b/.gitignore index 9e75cc10f..539da7c1d 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,3 @@ tool_test_output.html tool_test_output.json +.DS_Store diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml index 68205c04a..6c3117206 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml @@ -32,6 +32,7 @@ Name for Haplotype 1: Hap1 Name for Haplotype 2: Hap2 Homozygous Read Coverage: null + Database for Busco Lineage: v5 outputs: Hifiasm HiC hap1: assert: diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga index 46254fdae..0c1e60942 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga @@ -20,7 +20,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.2.1", + "release": "0.2.2", "name": "Assembly-Hifi-HiC-phasing-VGP4", "report": { "markdown": "\n# Workflow Execution Report\n\nTime workflow was invoked:\n\n```galaxy\ninvocation_time()\n```\nGalaxy version :\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Raw unitig graph\n\n```galaxy\nhistory_dataset_as_image(output=\"raw unitig graph image\")\n```\n\n## Merqury results\n\n### Merqury QV\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_qv\")\n```\n\n### Merqury completeness\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_stats\")\n```\n\n### Merqury plots\n\n\nspectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-cn.fl\")\n```\n\nspectra-asm:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-asm.fl\")\n```\n\nhap1 spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_01.spectra-cn.fl\")\n```\n\nhap2 spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_02.spectra-cn.fl\")\n```\n\n## BUSCO results (Vertebrata database)\n\nHap1\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary Image Hap1\")\n```\n\nHap2\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary Image Hap2\")\n```\n\n## Assembly statistics\n\n\n```galaxy\nhistory_dataset_as_table(output=\"clean_stats\")\n```\n\n\n## Nx and Size plots\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Nx Plot\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Size Plot\")\n```\n\n\n\n## Current Workflow\n```galaxy\nworkflow_display()\n```\n" @@ -162,11 +162,44 @@ "workflow_outputs": [] }, "5": { - "annotation": "Taxonomic lineage for the organism being assembled for Busco analysis", + "annotation": "", "content_id": null, "errors": null, "id": 5, "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Database for Busco Lineage" + } + ], + "label": "Database for Busco Lineage", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 81.55189123074645, + "top": 666.080035105452 + }, + "tool_id": null, + "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "245a5b51-c40d-4425-81ca-2baf3c157022", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "07c8cb5a-ff7f-4e51-8f81-74b2f7630f2e" + } + ] + }, + "6": { + "annotation": "Taxonomic lineage for the organism being assembled for Busco analysis", + "content_id": null, + "errors": null, + "id": 6, + "input_connections": {}, "inputs": [ { "description": "Taxonomic lineage for the organism being assembled for Busco analysis", @@ -177,8 +210,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 48.90625, - "top": 607.51953125 + "left": 112.31427690494708, + "top": 770.3740188995779 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", @@ -186,13 +219,19 @@ "type": "parameter_input", "uuid": "a9df063c-37ef-440d-93e6-212ac3a598e8", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "4c2b1889-3936-4df2-8375-250ca7dea2c7" + } + ] }, - "6": { + "7": { "annotation": "", "content_id": null, "errors": null, - "id": 6, + "id": 7, "input_connections": {}, "inputs": [ { @@ -204,8 +243,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 66.703125, - "top": 671.3125 + "left": 122.01184397539753, + "top": 852.6092753452594 }, "tool_id": null, "tool_state": "{\"default\": \"Hap1\", \"parameter_type\": \"text\", \"optional\": true}", @@ -213,13 +252,19 @@ "type": "parameter_input", "uuid": "41d1bb31-75f9-4034-abad-96aed4916b45", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "34ed45e3-2132-4c67-af2a-b72a8cbcf55c" + } + ] }, - "7": { + "8": { "annotation": "", "content_id": null, "errors": null, - "id": 7, + "id": 8, "input_connections": {}, "inputs": [ { @@ -231,8 +276,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 78.38870701261258, - "top": 769.8272396352553 + "left": 130.80851045942487, + "top": 939.8716854194543 }, "tool_id": null, "tool_state": "{\"default\": \"Hap2\", \"parameter_type\": \"text\", \"optional\": true}", @@ -240,13 +285,19 @@ "type": "parameter_input", "uuid": "6d5afa06-c3e8-4eb7-8819-8cfe8300c462", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "8c9ba587-c3e2-4200-8794-2b18ba08fc9e" + } + ] }, - "8": { + "9": { "annotation": "Defaults to 37 if not specified. For genomes much larger than human, applying -f38 or even -f39 is preferred to save memory on k-mer counting.", "content_id": null, "errors": null, - "id": 8, + "id": 9, "input_connections": {}, "inputs": [ { @@ -258,8 +309,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 96.0148601509567, - "top": 866.2253241049863 + "left": 137.2665356894154, + "top": 1033.0113085913417 }, "tool_id": null, "tool_state": "{\"default\": 37, \"parameter_type\": \"integer\", \"optional\": true}", @@ -267,13 +318,19 @@ "type": "parameter_input", "uuid": "b949921b-95a3-4d43-81b2-4006a4909e4b", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "0696f3a8-cd87-4b44-a71c-54611b53be34" + } + ] }, - "9": { + "10": { "annotation": "", "content_id": null, "errors": null, - "id": 9, + "id": 10, "input_connections": {}, "inputs": [ { @@ -285,8 +342,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 105.51087786212338, - "top": 966.1883445504246 + "left": 145.73965411666467, + "top": 1117.6864372730274 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": \"\"}", @@ -294,13 +351,19 @@ "type": "data_input", "uuid": "557a2e2b-008c-4566-836a-6509950aa85b", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "7b3c62fb-1823-4366-92b7-053ea9054620" + } + ] }, - "10": { + "11": { "annotation": "If empty, read coverage will be estimated from the Genomescope parameters. ", "content_id": null, "errors": null, - "id": 10, + "id": 11, "input_connections": {}, "inputs": [ { @@ -321,13 +384,19 @@ "type": "parameter_input", "uuid": "b251eddc-49e6-4899-a893-a904c29b9e75", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "2e143429-f516-4a3d-8983-08df349be75f" + } + ] }, - "11": { + "12": { "annotation": "GenomeScope model parameters generated by K-mer profiling workflow", "content_id": null, "errors": null, - "id": 11, + "id": 12, "input_connections": {}, "inputs": [ { @@ -350,11 +419,11 @@ "when": null, "workflow_outputs": [] }, - "12": { + "13": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "errors": null, - "id": 12, + "id": 13, "input_connections": { "library|input_1": { "id": 0, @@ -428,11 +497,11 @@ } ] }, - "13": { + "14": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1", "errors": null, - "id": 13, + "id": 14, "input_connections": { "infile": { "id": 3, @@ -473,14 +542,14 @@ "when": null, "workflow_outputs": [] }, - "14": { + "15": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0", "errors": null, - "id": 14, + "id": 15, "input_connections": { "input": { - "id": 11, + "id": 12, "output_name": "output" } }, @@ -518,14 +587,14 @@ "when": null, "workflow_outputs": [] }, - "15": { + "16": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", "errors": null, - "id": 15, + "id": 16, "input_connections": { "results_0|software_cond|input": { - "id": 12, + "id": 13, "output_name": "report" } }, @@ -561,14 +630,14 @@ "when": null, "workflow_outputs": [] }, - "16": { + "17": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "errors": null, - "id": 16, + "id": 17, "input_connections": { "infile": { - "id": 13, + "id": 14, "output_name": "output" } }, @@ -606,14 +675,14 @@ "when": null, "workflow_outputs": [] }, - "17": { + "18": { "annotation": "", "content_id": "Cut1", "errors": null, - "id": 17, + "id": 18, "input_connections": { "input": { - "id": 14, + "id": 15, "output_name": "out_file1" } }, @@ -645,14 +714,14 @@ "when": null, "workflow_outputs": [] }, - "18": { + "19": { "annotation": "", "content_id": "Convert characters1", "errors": null, - "id": 18, + "id": 19, "input_connections": { "input": { - "id": 16, + "id": 17, "output_name": "outfile" } }, @@ -684,14 +753,14 @@ "when": null, "workflow_outputs": [] }, - "19": { + "20": { "annotation": "", "content_id": "param_value_from_file", "errors": null, - "id": 19, + "id": 20, "input_connections": { "input1": { - "id": 17, + "id": 18, "output_name": "out_file1" } }, @@ -730,14 +799,14 @@ "when": null, "workflow_outputs": [] }, - "20": { + "21": { "annotation": "", "content_id": "Cut1", "errors": null, - "id": 20, + "id": 21, "input_connections": { "input": { - "id": 18, + "id": 19, "output_name": "out_file1" } }, @@ -769,18 +838,18 @@ "when": null, "workflow_outputs": [] }, - "21": { + "22": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, - "id": 21, + "id": 22, "input_connections": { "style_cond|type_cond|pick_from_0|value": { - "id": 10, + "id": 11, "output_name": "output" }, "style_cond|type_cond|pick_from_1|value": { - "id": 19, + "id": 20, "output_name": "integer_param" } }, @@ -820,14 +889,14 @@ "when": null, "workflow_outputs": [] }, - "22": { + "23": { "annotation": "", "content_id": "param_value_from_file", "errors": null, - "id": 22, + "id": 23, "input_connections": { "input1": { - "id": 20, + "id": 21, "output_name": "out_file1" } }, @@ -874,18 +943,18 @@ } ] }, - "23": { + "24": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0", "errors": null, - "id": 23, + "id": 24, "input_connections": { "assembly_options|hom_cov": { - "id": 21, + "id": 22, "output_name": "integer_param" }, "filter_bits": { - "id": 8, + "id": 9, "output_name": "output" }, "hic_partition|h1": { @@ -897,7 +966,7 @@ "output_name": "output" }, "mode|reads": { - "id": 12, + "id": 13, "output_name": "out1" } }, @@ -999,14 +1068,14 @@ "when": null, "workflow_outputs": [] }, - "24": { + "25": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4", "errors": null, - "id": 24, + "id": 25, "input_connections": { "input_file": { - "id": 23, + "id": 24, "output_name": "hic_raw_initig" } }, @@ -1052,18 +1121,18 @@ } ] }, - "25": { + "26": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 25, + "id": 26, "input_connections": { "input_file": { - "id": 23, + "id": 24, "output_name": "hic_balanced_contig_hap2_graph" }, "mode_condition|statistics_condition|expected_genomesize": { - "id": 22, + "id": 23, "output_name": "integer_param" } }, @@ -1110,18 +1179,18 @@ "when": null, "workflow_outputs": [] }, - "26": { + "27": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 26, + "id": 27, "input_connections": { "input_file": { - "id": 23, + "id": 24, "output_name": "hic_balanced_contig_hap1_graph" }, "mode_condition|statistics_condition|expected_genomesize": { - "id": 22, + "id": 23, "output_name": "integer_param" } }, @@ -1168,14 +1237,14 @@ "when": null, "workflow_outputs": [] }, - "27": { + "28": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 27, + "id": 28, "input_connections": { "input_file": { - "id": 23, + "id": 24, "output_name": "hic_balanced_contig_hap2_graph" } }, @@ -1222,14 +1291,14 @@ "when": null, "workflow_outputs": [] }, - "28": { + "29": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 28, + "id": 29, "input_connections": { "input_file": { - "id": 23, + "id": 24, "output_name": "hic_balanced_contig_hap2_graph" } }, @@ -1282,14 +1351,14 @@ } ] }, - "29": { + "30": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 29, + "id": 30, "input_connections": { "input_file": { - "id": 23, + "id": 24, "output_name": "hic_balanced_contig_hap1_graph" } }, @@ -1336,14 +1405,14 @@ "when": null, "workflow_outputs": [] }, - "30": { + "31": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 30, + "id": 31, "input_connections": { "input_file": { - "id": 23, + "id": 24, "output_name": "hic_balanced_contig_hap1_graph" } }, @@ -1396,18 +1465,18 @@ } ] }, - "31": { + "32": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 31, + "id": 32, "input_connections": { "input_file": { - "id": 23, + "id": 24, "output_name": "hic_balanced_contig_hap2_graph" }, "mode_condition|swiss_army_knife": { - "id": 9, + "id": 10, "output_name": "output" } }, @@ -1445,18 +1514,18 @@ "when": null, "workflow_outputs": [] }, - "32": { + "33": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 32, + "id": 33, "input_connections": { "input_file": { - "id": 23, + "id": 24, "output_name": "hic_balanced_contig_hap1_graph" }, "mode_condition|swiss_army_knife": { - "id": 9, + "id": 10, "output_name": "output" } }, @@ -1494,14 +1563,14 @@ "when": null, "workflow_outputs": [] }, - "33": { + "34": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "errors": null, - "id": 33, + "id": 34, "input_connections": { "infile": { - "id": 25, + "id": 26, "output_name": "stats" } }, @@ -1539,14 +1608,14 @@ "when": null, "workflow_outputs": [] }, - "34": { + "35": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "errors": null, - "id": 34, + "id": 35, "input_connections": { "infile": { - "id": 26, + "id": 27, "output_name": "stats" } }, @@ -1584,12 +1653,12 @@ "when": null, "workflow_outputs": [] }, - "35": { + "36": { "annotation": "", - "id": 35, + "id": 36, "input_connections": { "gfa_stats": { - "id": 27, + "id": 28, "input_subworkflow_step_id": 0, "output_name": "stats" } @@ -1966,12 +2035,12 @@ "when": null, "workflow_outputs": [] }, - "36": { + "37": { "annotation": "", - "id": 36, + "id": 37, "input_connections": { "gfa_stats": { - "id": 29, + "id": 30, "input_subworkflow_step_id": 0, "output_name": "stats" } @@ -2348,14 +2417,14 @@ "when": null, "workflow_outputs": [] }, - "37": { + "38": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1", "errors": null, - "id": 37, + "id": 38, "input_connections": { "infile": { - "id": 31, + "id": 32, "output_name": "output" } }, @@ -2408,14 +2477,14 @@ } ] }, - "38": { + "39": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1", "errors": null, - "id": 38, + "id": 39, "input_connections": { "infile": { - "id": 32, + "id": 33, "output_name": "output" } }, @@ -2468,18 +2537,18 @@ } ] }, - "39": { + "40": { "annotation": "", "content_id": "join1", "errors": null, - "id": 39, + "id": 40, "input_connections": { "input1": { - "id": 34, + "id": 35, "output_name": "outfile" }, "input2": { - "id": 33, + "id": 34, "output_name": "outfile" } }, @@ -2511,27 +2580,27 @@ "when": null, "workflow_outputs": [] }, - "40": { + "41": { "annotation": "", - "id": 40, + "id": 41, "input_connections": { "Alternate data": { - "id": 35, + "id": 36, "input_subworkflow_step_id": 1, "output_name": "gfastats data for plotting" }, "Name of alternate assembly": { - "id": 7, + "id": 8, "input_subworkflow_step_id": 3, "output_name": "output" }, "Name of primary assembly": { - "id": 6, + "id": 7, "input_subworkflow_step_id": 2, "output_name": "output" }, "Primary data": { - "id": 36, + "id": 37, "input_subworkflow_step_id": 0, "output_name": "gfastats data for plotting" } @@ -3054,19 +3123,23 @@ } ] }, - "41": { + "42": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0", "errors": null, - "id": 41, + "id": 42, "input_connections": { "input": { - "id": 37, + "id": 38, "output_name": "output" }, - "lineage|lineage_dataset": { + "lineage_conditional|cached_db": { "id": 5, "output_name": "output" + }, + "lineage|lineage_dataset": { + "id": 6, + "output_name": "output" } }, "inputs": [], @@ -3142,16 +3215,16 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"cached\", \"__current_case__\": 0, \"cached_db\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "5.5.0+galaxy0", "type": "tool", "uuid": "08066bc3-0992-4606-844d-16be3c56691a", "when": null, "workflow_outputs": [ { - "label": "Busco Summary Image Hap2", - "output_name": "summary_image", - "uuid": "84725fc4-3480-44a2-abc0-abc8f54addb1" + "label": "Busco Gff File - Hap2", + "output_name": "busco_gff", + "uuid": "3b8e8b67-ad7d-4d30-a253-e601d3e201d2" }, { "label": "Busco Summary Hap2", @@ -3159,24 +3232,24 @@ "uuid": "bf7e959c-5252-467e-bb58-2b8cabbd0f3b" }, { - "label": "Busco Gff File - Hap2", - "output_name": "busco_gff", - "uuid": "3b8e8b67-ad7d-4d30-a253-e601d3e201d2" + "label": "Busco Summary Image Hap2", + "output_name": "summary_image", + "uuid": "84725fc4-3480-44a2-abc0-abc8f54addb1" } ] }, - "42": { + "43": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4", "errors": null, - "id": 42, + "id": 43, "input_connections": { "mode|assembly_options|assembly_01": { - "id": 38, + "id": 39, "output_name": "output" }, "mode|assembly_options|assembly_02": { - "id": 37, + "id": 38, "output_name": "output" }, "mode|meryldb_F1": { @@ -3282,6 +3355,11 @@ "uuid": "9985e575-3113-4c2c-bc2c-78faab3a1291", "when": null, "workflow_outputs": [ + { + "label": "Merqury Stats", + "output_name": "stats_files", + "uuid": "22a82fae-74cf-4024-9815-ba6a9892aac3" + }, { "label": "Merqury images", "output_name": "png_files", @@ -3296,27 +3374,26 @@ "label": "Merqury QV", "output_name": "qv_files", "uuid": "5ba07c29-6ca5-42bd-a1e8-f4f6a35c3814" - }, - { - "label": "Merqury Stats", - "output_name": "stats_files", - "uuid": "22a82fae-74cf-4024-9815-ba6a9892aac3" } ] }, - "43": { + "44": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0", "errors": null, - "id": 43, + "id": 44, "input_connections": { "input": { - "id": 38, + "id": 39, "output_name": "output" }, - "lineage|lineage_dataset": { + "lineage_conditional|cached_db": { "id": 5, "output_name": "output" + }, + "lineage|lineage_dataset": { + "id": 6, + "output_name": "output" } }, "inputs": [], @@ -3345,8 +3422,8 @@ } ], "position": { - "left": 2568.723853333207, - "top": 1078.3517946538443 + "left": 2599.0485857103813, + "top": 1053.6223175775656 }, "post_job_actions": { "TagDatasetActionbusco_gff": { @@ -3392,16 +3469,16 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"cached\", \"__current_case__\": 0, \"cached_db\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "5.5.0+galaxy0", "type": "tool", "uuid": "a4957dee-45cc-4f34-ae2e-e07f93b9fcc4", "when": null, "workflow_outputs": [ { - "label": "Busco Summary Image Hap1", - "output_name": "summary_image", - "uuid": "cfac3083-4c1e-4bb4-91a5-eba5d19f2757" + "label": "Busco Summary Hap1", + "output_name": "busco_sum", + "uuid": "bd6443ea-5266-4dfc-8f1e-aded27317da8" }, { "label": "Busco Gff File - Hap1", @@ -3409,20 +3486,20 @@ "uuid": "ba26cb24-25d4-4669-982c-abe4816753a6" }, { - "label": "Busco Summary Hap1", - "output_name": "busco_sum", - "uuid": "bd6443ea-5266-4dfc-8f1e-aded27317da8" + "label": "Busco Summary Image Hap1", + "output_name": "summary_image", + "uuid": "cfac3083-4c1e-4bb4-91a5-eba5d19f2757" } ] }, - "44": { + "45": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1", "errors": null, - "id": 44, + "id": 45, "input_connections": { "input": { - "id": 39, + "id": 40, "output_name": "out_file1" } }, @@ -3475,14 +3552,14 @@ } ] }, - "45": { + "46": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 45, + "id": 46, "input_connections": { "input": { - "id": 42, + "id": 43, "output_name": "png_files" } }, @@ -3520,14 +3597,14 @@ } ] }, - "46": { + "47": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 46, + "id": 47, "input_connections": { "input": { - "id": 42, + "id": 43, "output_name": "png_files" } }, @@ -3565,14 +3642,14 @@ } ] }, - "47": { + "48": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 47, + "id": 48, "input_connections": { "input": { - "id": 42, + "id": 43, "output_name": "qv_files" } }, @@ -3610,14 +3687,14 @@ } ] }, - "48": { + "49": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 48, + "id": 49, "input_connections": { "input": { - "id": 42, + "id": 43, "output_name": "png_files" } }, @@ -3655,14 +3732,14 @@ } ] }, - "49": { + "50": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 49, + "id": 50, "input_connections": { "input": { - "id": 42, + "id": 43, "output_name": "stats_files" } }, @@ -3700,14 +3777,14 @@ } ] }, - "50": { + "51": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 50, + "id": 51, "input_connections": { "input": { - "id": 42, + "id": 43, "output_name": "png_files" } }, @@ -3745,14 +3822,14 @@ } ] }, - "51": { + "52": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "errors": null, - "id": 51, + "id": 52, "input_connections": { "infile": { - "id": 44, + "id": 45, "output_name": "output" } }, @@ -3801,6 +3878,6 @@ "VGP", "Reviewed" ], - "uuid": "4135d455-ac66-4d86-b4a3-643580ff877f", - "version": 5 -} + "uuid": "cb0e2983-13df-451c-85a2-ee78c94a2bd2", + "version": 1 +} \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md index 06dad0676..048600877 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md @@ -1,5 +1,9 @@ # Changelog +## [0.2.2] 2024-08-07 + +- Expose parameter: Busco lineage database + ## [0.2.1] 2024-07-29 ### Automatic update diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5-tests.yml b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5-tests.yml index 1300eae42..8b77724e8 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5-tests.yml +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5-tests.yml @@ -52,6 +52,7 @@ Bits for bloom filter: 32 Name for Haplotype 1: Hap1 Name for Haplotype 2: Hap2 + Database for Busco Lineage: v5 Lineage: vertebrata_odb10 outputs: Estimated Genome size: 2288021 diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga index f13aee696..d9b21ec9f 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga @@ -15,8 +15,11 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.1.8", + "release": "0.2", "name": "Assembly-Hifi-Trio-phasing-VGP5", + "report": { + "markdown": "\n# Workflow Execution Report\n\nTime workflow was invoked:\n\n```galaxy\ninvocation_time()\n```\nGalaxy version :\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Raw unitig graph\n\n```galaxy\nhistory_dataset_as_image(output=\"raw unitig graph image\")\n```\n\n## Merqury results\n\n### Merqury QV\n\n```galaxy\nhistory_dataset_as_table(output=merqury_stats)\n```\n\n### Merqury completeness\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_stats\")\n```\n\n### Merqury plots\n\n\nspectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-cn.fl\")\n```\n\nspectra-asm:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-asm.fl\")\n```\n\n\nhap1 spectra-cn:\n\n\r\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_01.spectra-cn.fl\")\n```\r\n\n\nhap2 spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_02.spectra-cn.fl\")\n```\n\n## BUSCO results (Vertebrata database)\n\nHap1\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary Image Hap1\")\n```\n\nHap2\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary Image Hap2\")\n```\n\n## Assembly statistics\n\n\n```galaxy\nhistory_dataset_as_table(output=\"clean_stats\")\n```\n\n\n## Nx and Size plots\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Nx Plot\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Size Plot\")\n```\n\n\n\n## Current Workflow\n```galaxy\nworkflow_display()\n```\n" + }, "steps": { "0": { "annotation": "", @@ -196,8 +199,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 16.973703852699934, - "top": 875.4758102675167 + "left": 14.278967454027603, + "top": 893.0522085856591 }, "tool_id": null, "tool_state": "{\"default\": 37, \"parameter_type\": \"integer\", \"optional\": true}", @@ -205,14 +208,53 @@ "type": "parameter_input", "uuid": "a5987ed3-6fdb-49c7-92d0-5b2f78a9bbb9", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "1bb5df96-d731-4e12-b902-ec6e1d723b07" + } + ] }, "7": { - "annotation": "Taxonomic lineage for the organism being assembled for Busco analysis", + "annotation": "", "content_id": null, "errors": null, "id": 7, "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Database for Busco Lineage" + } + ], + "label": "Database for Busco Lineage", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 28.142955132748718, + "top": 1078.9295496884674 + }, + "tool_id": null, + "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "ca553be3-e5c9-4770-bd61-d50ed05c69ae", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "9829d67c-d793-44c9-9b53-9c3ebd2155a8" + } + ] + }, + "8": { + "annotation": "Taxonomic lineage for the organism being assembled for Busco analysis", + "content_id": null, + "errors": null, + "id": 8, + "input_connections": {}, "inputs": [ { "description": "Taxonomic lineage for the organism being assembled for Busco analysis", @@ -223,8 +265,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 36.34366195032787, - "top": 998.1239416236981 + "left": 61.152110333438976, + "top": 1189.4200518565176 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", @@ -232,13 +274,19 @@ "type": "parameter_input", "uuid": "9762d451-eb6f-4f0c-8203-7094f46ea771", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "9dff2868-bf8a-4443-87c9-52f5b8975bdb" + } + ] }, - "8": { + "9": { "annotation": "If empty, read coverage will be estimated from the Genomescope parameters. ", "content_id": null, "errors": null, - "id": 8, + "id": 9, "input_connections": {}, "inputs": [ { @@ -250,8 +298,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 65.73786407849795, - "top": 1111.7501052118992 + "left": 98.92882500063175, + "top": 1275.4014318043698 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"integer\", \"optional\": true}", @@ -259,13 +307,19 @@ "type": "parameter_input", "uuid": "ffcf874f-594d-4d58-99dc-73ef566bcc88", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "28a260f0-a63e-4743-ba41-6544e4f423a9" + } + ] }, - "9": { + "10": { "annotation": "GenomeScope model parameters generated by K-mer profiling workflow", "content_id": null, "errors": null, - "id": 9, + "id": 10, "input_connections": {}, "inputs": [ { @@ -277,8 +331,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 101.3532659049146, - "top": 1219.9729028733702 + "left": 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"label": "cutadapt multiqc stats", "output_name": "stats", "uuid": "110b5141-3025-4ee6-8d4a-d4987fa6dfe5" + }, + { + "label": "multiqc html report", + "output_name": "html_report", + "uuid": "9bd9c4ff-97c3-4557-a550-a360207e08ab" } ] }, - "19": { + "20": { "annotation": "", "content_id": "Cut1", "errors": null, - "id": 19, + "id": 20, "input_connections": { "input": { - "id": 16, + "id": 17, "output_name": "out_file1" } }, @@ -679,14 +757,14 @@ "when": null, "workflow_outputs": [] }, - "20": { + "21": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "errors": null, - "id": 20, + "id": 21, "input_connections": { "infile": { - "id": 17, + "id": 18, "output_name": "output" } }, @@ -724,14 +802,14 @@ "when": null, "workflow_outputs": [] }, - "21": { + "22": { "annotation": "", "content_id": "param_value_from_file", "errors": null, - "id": 21, + "id": 22, "input_connections": { "input1": { - "id": 19, + "id": 20, "output_name": "out_file1" } }, @@ -763,14 +841,14 @@ "when": null, "workflow_outputs": [] }, - "22": { + "23": { "annotation": "", "content_id": "Convert characters1", "errors": null, - "id": 22, + "id": 23, "input_connections": { "input": { - "id": 20, + "id": 21, "output_name": "outfile" } }, @@ -802,18 +880,18 @@ "when": null, "workflow_outputs": [] }, - "23": { + "24": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, - "id": 23, + "id": 24, "input_connections": { "style_cond|type_cond|pick_from_0|value": { - "id": 8, + "id": 9, "output_name": "output" }, "style_cond|type_cond|pick_from_1|value": { - "id": 21, + "id": 22, "output_name": "integer_param" } }, @@ -853,14 +931,14 @@ "when": null, "workflow_outputs": [] }, - "24": { + "25": { "annotation": "", "content_id": "Cut1", "errors": null, - "id": 24, + "id": 25, "input_connections": { "input": { - "id": 22, + "id": 23, "output_name": "out_file1" } }, @@ -892,14 +970,14 @@ "when": null, "workflow_outputs": [] }, - "25": { + "26": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0", "errors": null, - "id": 25, + "id": 26, "input_connections": { "assembly_options|hom_cov": { - "id": 23, + "id": 24, "output_name": "integer_param" }, "filter_bits": { @@ -907,11 +985,11 @@ "output_name": "output" }, "mode|reads": { - "id": 15, + "id": 16, "output_name": "out1" }, "mode|trio_dual": { - "id": 11, + "id": 12, "output_name": "output" }, "mode|trioinput|hap1_reads": { @@ -1014,14 +1092,14 @@ "when": null, "workflow_outputs": [] }, - "26": { + "27": { "annotation": "", "content_id": "param_value_from_file", "errors": null, - "id": 26, + "id": 27, "input_connections": { "input1": { - "id": 24, + "id": 25, "output_name": "out_file1" } }, @@ -1068,18 +1146,18 @@ } ] }, - "27": { + "28": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 27, + "id": 28, "input_connections": { "input_file": { - "id": 25, + "id": 26, "output_name": "hap1_contigs" }, "mode_condition|swiss_army_knife": { - "id": 12, + "id": 13, "output_name": "output" } }, @@ -1132,18 +1210,18 @@ } ] }, - "28": { + "29": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 28, + "id": 29, "input_connections": { "input_file": { - "id": 25, + "id": 26, "output_name": "hap2_contigs" }, "mode_condition|swiss_army_knife": { - "id": 12, + "id": 13, "output_name": "output" } }, @@ -1196,14 +1274,14 @@ } ] }, - "29": { + "30": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4", "errors": null, - "id": 29, + "id": 30, "input_connections": { "input_file": { - "id": 25, + "id": 26, "output_name": "raw_unitigs_trio" } }, @@ -1241,20 +1319,26 @@ "type": "tool", "uuid": "f9af6aa8-4ee4-4d4d-a54f-653881706285", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": "raw unitig graph image", + "output_name": "outfile", + "uuid": "c5d8c5b8-3d33-473d-96bc-cedd33d14786" + } + ] }, - "30": { + "31": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 30, + "id": 31, "input_connections": { "input_file": { - "id": 25, + "id": 26, "output_name": "hap1_contigs" }, "mode_condition|swiss_army_knife": { - "id": 12, + "id": 13, "output_name": "output" } }, @@ -1321,18 +1405,18 @@ } ] }, - "31": { + "32": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 31, + "id": 32, "input_connections": { "input_file": { - "id": 25, + "id": 26, "output_name": "hap2_contigs" }, "mode_condition|swiss_army_knife": { - "id": 12, + "id": 13, "output_name": "output" } }, @@ -1399,14 +1483,14 @@ } ] }, - "32": { + "33": { "annotation": "", "content_id": 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"owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"#\", \"replace_pattern\": \"Number of\", \"is_regex\": false, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "9.3+galaxy1", + "type": "tool", + "uuid": "68545a0f-7aa4-43e3-bf1a-5dcb75108c51", + "when": null, + "workflow_outputs": [ + { + "label": "clean_stats", + "output_name": "outfile", + "uuid": "fe375d8e-3e97-4373-b3ac-0d2e409d0145" } ] } @@ -3425,6 +3899,6 @@ "VGP", "Reviewed" ], - "uuid": "d8fd9266-a2f8-4a6e-9c12-8d312bdd2ca7", - "version": 6 -} + "uuid": "3cacf798-0f32-43b9-82c0-2d8f76312c80", + "version": 8 +} \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md index 353004091..084dab9b6 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md @@ -1,5 +1,16 @@ # Changelog +## [0.2] 2024-08-12 + +### Added + +- Workflow report + +### Changed + +- Expose the Busco lineage database parameter +- Fix a bug happening when merging assembly statistics : The presence of the '#' character caused the tables to join incorrectly, and the numbers did not match the metrics + ## [0.1.8] 2024-07-22 ### Automatic update diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml index be09fe98d..f00fcbb5b 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml @@ -23,6 +23,7 @@ Bits for Hifiasm bloom filter: 32 SAK input file (Optional): null Homozygous Read Coverage: null + Database for Busco Lineage: v5 Lineage: vertebrata_odb10 Name of primary assembly: Primary Name of alternate assembly: Alternate @@ -44,6 +45,10 @@ asserts: has_line: line: "# scaffolds 85" + Assembly statistics: + asserts: + has_line: + line: "# scaffolds 85 1" Nx Plot: asserts: has_size: diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga index 5651859cd..136b94576 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga @@ -15,8 +15,11 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.1.8", + "release": "0.2.1", "name": "Assembly-Hifi-only-VGP3", + "report": { + "markdown": "\n# Workflow Execution Report\n\nTime workflow was invoked:\n\n```galaxy\ninvocation_time()\n```\nGalaxy version :\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Raw unitig graph\n\n```galaxy\nhistory_dataset_as_image(output=\"raw unitig graph image\")\n```\n\n## Merqury results\n\n### Merqury QV\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_qv\")\n```\n\n### Merqury completeness\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_stats\")\n```\n\n### Merqury plots\n\n\nspectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-cn.fl\")\n```\n\nspectra-asm:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-asm.fl\")\n```\n\nhap1 spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_01.spectra-cn.fl\")\n```\n\n\n## BUSCO results (Vertebrata database)\n\n\n\n## Assembly statistics\n\n\n```galaxy\nhistory_dataset_as_table(output=\"clean_stats\")\n```\n\n\n## Nx and Size plots\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Nx Plot\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Size Plot\")\n```\n\n\n\n## Current Workflow\n```galaxy\nworkflow_display()\n```\n" + }, "steps": { "0": { "annotation": "", @@ -181,11 +184,38 @@ "workflow_outputs": [] }, "6": { - "annotation": "Taxonomic lineage for the organism being assembled for Busco analysis", + "annotation": "", "content_id": null, "errors": null, "id": 6, "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Database for Busco Lineage" + } + ], + "label": "Database for Busco Lineage", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 422.96681360823476, + "top": 1352.5435082963184 + }, + "tool_id": null, + "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "af7ad6ad-2718-4a16-ad1f-6858b1b4fb50", + "when": null, + "workflow_outputs": [] + }, + "7": { + "annotation": "Taxonomic lineage for the organism being assembled for Busco analysis", + "content_id": null, + "errors": null, + "id": 7, + "input_connections": {}, "inputs": [ { "description": "Taxonomic lineage for the organism being assembled for Busco analysis", @@ -196,8 +226,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 432.9672084074356, - "top": 1396.376653536473 + "left": 500.2702810213637, + "top": 1472.6772609095954 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", @@ -207,11 +237,11 @@ "when": null, "workflow_outputs": [] }, - "7": { + "8": { "annotation": "", "content_id": null, "errors": null, - "id": 7, + "id": 8, "input_connections": {}, "inputs": [ { @@ -234,11 +264,11 @@ "when": null, "workflow_outputs": [] }, - "8": { + "9": { "annotation": "", "content_id": null, "errors": null, - "id": 8, + "id": 9, "input_connections": {}, "inputs": [ { @@ -261,11 +291,11 @@ "when": null, "workflow_outputs": [] }, - "9": { + "10": { "annotation": "", "content_id": null, "errors": null, - "id": 9, + "id": 10, "input_connections": {}, "inputs": [ { @@ -288,11 +318,11 @@ "when": null, "workflow_outputs": [] }, - "10": { + "11": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "errors": null, - "id": 10, + "id": 11, "input_connections": { "library|input_1": { "id": 0, @@ -348,11 +378,11 @@ "when": null, "workflow_outputs": [] }, - "11": { + "12": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1", "errors": null, - "id": 11, + "id": 12, "input_connections": { "infile": { "id": 2, @@ -393,11 +423,11 @@ "when": null, "workflow_outputs": [] }, - "12": { + "13": { "annotation": "", "content_id": 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"input_connections": { "infile": { - "id": 11, + "id": 12, "output_name": "output" } }, @@ -576,14 +606,14 @@ "when": null, "workflow_outputs": [] }, - "16": { + "17": { "annotation": "", "content_id": "Cut1", "errors": null, - "id": 16, + "id": 17, "input_connections": { "input": { - "id": 13, + "id": 14, "output_name": "out_file1" } }, @@ -615,14 +645,14 @@ "when": null, "workflow_outputs": [] }, - "17": { + "18": { "annotation": "", "content_id": "Convert characters1", "errors": null, - "id": 17, + "id": 18, "input_connections": { "input": { - "id": 15, + "id": 16, "output_name": "outfile" } }, @@ -654,14 +684,14 @@ "when": null, "workflow_outputs": [] }, - "18": { + "19": { "annotation": "", "content_id": "param_value_from_file", "errors": null, - "id": 18, + "id": 19, "input_connections": { "input1": { - "id": 16, + "id": 17, "output_name": "out_file1" } }, @@ -695,14 +725,14 @@ "when": null, "workflow_outputs": [] }, - "19": { + "20": { "annotation": "", "content_id": "Cut1", "errors": null, - "id": 19, + "id": 20, "input_connections": { "input": { - "id": 17, + "id": 18, "output_name": "out_file1" } }, @@ -734,18 +764,18 @@ "when": null, "workflow_outputs": [] }, - "20": { + "21": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, - "id": 20, + "id": 21, "input_connections": { "style_cond|type_cond|pick_from_0|value": { "id": 4, "output_name": "output" }, "style_cond|type_cond|pick_from_1|value": { - "id": 18, + "id": 19, "output_name": "integer_param" } }, @@ -785,14 +815,14 @@ "when": null, "workflow_outputs": [] }, - "21": { + "22": { "annotation": "", "content_id": "param_value_from_file", "errors": null, - "id": 21, + "id": 22, "input_connections": { "input1": { - "id": 19, + "id": 20, "output_name": "out_file1" } }, @@ -839,22 +869,22 @@ } ] }, - "22": { + "23": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0", "errors": null, - 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"output_name": "alternate_contig_graph" }, "mode_condition|swiss_army_knife": { - "id": 7, + "id": 8, "output_name": "output" } }, @@ -1017,18 +1100,18 @@ } ] }, - "24": { + "26": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 24, + "id": 26, "input_connections": { "input_file": { - "id": 22, + "id": 23, "output_name": "primary_contig_graph" }, "mode_condition|swiss_army_knife": { - "id": 7, + "id": 8, "output_name": "output" } }, @@ -1081,18 +1164,18 @@ } ] }, - "25": { + "27": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 25, + "id": 27, "input_connections": { "input_file": { - "id": 22, + "id": 23, "output_name": "primary_contig_graph" }, "mode_condition|swiss_army_knife": { - "id": 7, + "id": 8, "output_name": "output" } }, @@ -1152,18 +1235,18 @@ } ] }, - "26": { + "28": { "annotation": "", "content_id": 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\"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "9.3+galaxy1", + "type": "tool", + "uuid": "ec90b8f9-bcc2-4b8a-88ee-03b3e19979ba", + "when": null, + "workflow_outputs": [ + { + "label": "clean_stats", + "output_name": "outfile", + "uuid": "365867c1-fec9-4c10-8b31-3f615992910a" } ] } @@ -3135,6 +3538,6 @@ "VGP", "Reviewed" ], - "uuid": "f6f4cac5-6900-440b-8f1d-52420f635420", + "uuid": "2988562a-fa7a-4135-bf67-943ab03d1517", "version": 1 -} +} \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md index d755205a9..cac117d0b 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md @@ -1,5 +1,20 @@ # Changelog +## [0.2.1] 2024-08-13 + +- Expose Busco lineage database parameter + +## [0.2] 2024-08-01 + +### Added + +- Add bandage image +- Add workflow report + +### Changed + +- Fix bug in merging assembly statistics + ## [0.1.8] 2024-07-22 ### Automatic update diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/README.md b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/README.md index 47180d7c5..8d24d78ca 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/README.md +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/README.md @@ -1,26 +1,29 @@ -## Contiging Solo w/HiC: +## Contiging Solo: -Generate phased assembly based on PacBio Hifi Reads using HiC data from the same individual for phasing. +Generate assembly based on PacBio Hifi Reads. ### Inputs 1. Hifi long reads [fastq] -2. HiC forward reads (if multiple input files, concatenated in same order as reverse reads) [fastq] -3. HiC reverse reads (if multiple input files, concatenated in same order as forward reads) [fastq] -4. K-mer database [meryldb] -5. Genome profile summary generated by Genomescope [txt] -6. Name of first assembly -7. Name of second assembly +2. K-mer database [meryldb] +3. Genome profile summary generated by Genomescope [txt] +4. Homozygous Read Coverage. Optional, use if you think the estimation from Genomescope is inacurate. +5. Genomescope Model Parameters generated by Genomescope [tabular] +6. Database for busco lineage (recommended: latest) +7. Busco lineage (recommended: vertebrata) +8. Name of first assembly +9. Name of second assembly ### Outputs -1. Haplotype 1 assembly -2. Haplotype 2 assembly -3. QC: BUSCO report for both assemblies -4. QC: Merqury report for both assemblies -5. QC: Assembly statistics for both assemblies -6. QC: Nx plot for both assemblies -7. QC: Size plot for both assemblie +1. Primary assembly +2. Alternate assembly +3. QC: Bandage image for the raw unitigs +4. QC: BUSCO report for both assemblies +5. QC: Merqury report for both assemblies +6. QC: Assembly statistics for both assemblies +7. QC: Nx plot for both assemblies +8. QC: Size plot for both assemblie diff --git a/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9-tests.yml b/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9-tests.yml index e0f853eb5..9ad050ede 100644 --- a/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9-tests.yml +++ b/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9-tests.yml @@ -2,16 +2,20 @@ job: Scaffolded assembly (fasta): class: File - location: https://zenodo.org/records/10067431/files/Scaffolded_assembly.fasta?download=1 + location: https://zenodo.org/records/13327557/files/Scaffolded_assembly.fasta?download=1 filetype: fasta Database for Kraken2: viral2019-03 outputs: - full contaminant + mito scaffold list: - file: test-data/full contaminant + mito scaffold list.txt - compare: diff - sort: true + mito_scaff_names: + asserts: + has_text: + text: "scaffold_82" final decontaminated assembly: decompress: true asserts: not_has_text: - text: "_1100" + text: "scaffold_200" + contaminants_table: + asserts: + has_text: + text: "scaffold_200" diff --git a/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9.ga b/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9.ga index b83991631..4e2cbc599 100644 --- a/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9.ga +++ b/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9.ga @@ -11,8 +11,11 @@ ], "format-version": "0.1", "license": "BSD-3-Clause", - "release": "0.1.6", + "release": "0.3", "name": "Assembly-decontamination-VGP9", + "report": { + "markdown": "\n# Workflow Execution Report\n\n### Worflow ran on: \n\n```galaxy\ninvocation_time()\n```\n\n# List of contaminants\n\n\r\n```galaxy\nhistory_dataset_as_table(output=\"contaminants_table\")\n```\r\n\n\n# List of Mitochondrial scaffolds\n\r\n```galaxy\nhistory_dataset_as_table(output=\"mito_scaff_names\")\n```\r\n\n\n\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" + }, "steps": { "0": { "annotation": "", @@ -30,8 +33,8 @@ "name": "Input dataset", "outputs": [], "position": { - 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"12": { + "10": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1", "errors": null, - "id": 12, + "id": 10, "input_connections": { "inputs": [ { - "id": 10, - "output_name": "output" + "id": 7, + "output_name": "mito_scaff_names" }, { - "id": 11, - "output_name": "outfile" + "id": 9, + "output_name": "out_file1" } ] }, @@ -543,13 +482,13 @@ } ], "position": { - "left": 2611.0546875, - "top": 276.36328125 + "left": 2538.6178936709443, + "top": 423.9453125 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -567,18 +506,18 @@ } ] }, - "13": { + "11": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 13, + "id": 11, "input_connections": { "input_file": { "id": 0, "output_name": "output" }, "target_condition|exclude_bed": { - "id": 12, + "id": 10, "output_name": "out_file1" } }, @@ -592,8 +531,8 @@ } ], "position": { - "left": 3050.21875, - "top": 650.49609375 + "left": 2977.7819561709443, + "top": 798.078125 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", @@ -620,6 +559,6 @@ "tags": [ "VGP_curated" ], - "uuid": "f6d8df21-f1dc-493c-bfab-e2cbecb8873d", - "version": 1 -} + "uuid": "aa4960d9-198d-4990-a393-a98efcd3070a", + "version": 3 +} \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/CHANGELOG.md index 3414f50e8..f9eaf2e64 100644 --- a/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/CHANGELOG.md @@ -1,5 +1,14 @@ # Changelog +## [0.3] 2024-08-26 + +- Changed the regex to only change the sequences. The workflow is now more robust to different (non VGP) scaffold names and VGP names with prefixes. +- Reduce the number of steps in the workflow. + +## [0.2] 2024-08-15 + +- Bug Fix: a missing regex caused the list of contaminants to empty out and the contaminants were not removed. + ## [0.1.6] 2024-06-10 ### Automatic update diff --git a/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/test-data/full contaminant + mito scaffold list.txt b/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/test-data/full contaminant + mito scaffold list.txt deleted file mode 100644 index 50433e8b3..000000000 --- a/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/test-data/full contaminant + mito scaffold list.txt +++ /dev/null @@ -1,2 +0,0 @@ -scaffold_1058 -scaffold_1100 diff --git a/workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/Mitogenome-Assembly-VGP0-tests.yml b/workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/Mitogenome-Assembly-VGP0-tests.yml index 9ed2a53dd..8a5cfd2a7 100644 --- a/workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/Mitogenome-Assembly-VGP0-tests.yml +++ b/workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/Mitogenome-Assembly-VGP0-tests.yml @@ -25,6 +25,6 @@ value: 68000 delta: 5000 mitogenome_genbank: - assert: - has_n_line: + asserts: + has_n_lines: n: 480 diff --git a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md index 49615216c..89ecef563 100644 --- a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md @@ -1,5 +1,15 @@ # Changelog +## [0.4] 2024-08-13 + +### Added + +- Workflow report + +### Changed + +- Expose Busco lineage database parameter +- Fix bug that was causing issues when merging the assembly statistics: The presence of the '#' character caused the tables to join incorrectly, and the numbers did not match the metrics ## [0.3.8] 2024-04-23 diff --git a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP-tests.yml b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP-tests.yml index d0439c476..9d16908f2 100644 --- a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP-tests.yml +++ b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP-tests.yml @@ -27,6 +27,7 @@ - class: File identifier: yeast_reads_sub1.fastq.gz location: https://zenodo.org/records/10047837/files/Pacbio%20Reads%20Collection%20-%20Trimmed_yeast_reads_sub1.fastq.gz.fastq.gz?download=1 + Database for Busco Lineage: v5 Lineage: vertebrata_odb10 Name of primary assembly: Primary Name of alternate assembly: Alternate diff --git a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6.ga b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6.ga index a004fd2a2..e6b6960f2 100644 --- a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6.ga +++ b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6.ga @@ -15,8 +15,11 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.3.8", + "release": "0.4", "name": "Purge-duplicate-contigs-VGP6", + "report": { + "markdown": "\n# Workflow Execution Report\n\nTime workflow was invoked\n\n```galaxy\ninvocation_time()\n```\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Merqury results\n\nMerqury QV:\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_QV\")\n```\n\nMerqury completeness:\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_stats\")\n```\n\nMerqury plots:\n\nspectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-cn.fl\")\n```\n\n\nspectra-asm:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-asm.fl\")\n```\n\n\nhap1/Primary spectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_01.spectra-cn.fl\")\n```\n\n\nhap2/alternate spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_02.spectra-cn.fl\")\n```\n\n\n\n\n## BUSCO results (Vertebrata database)\n\nPurged hap1/primary Assembly\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco on Purged Primary assembly: summary image\")\n```\n\n\n## Assembly statistics\n\n\n```galaxy\nhistory_dataset_as_table(output=\"clean_stats\")\n```\n\n\n## Nx and Size plots\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Nx Plot\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Size Plot\")\n```\n\n\n\n## Current Workflow\n```galaxy\nworkflow_display()\n```\n" + }, "steps": { "0": { "annotation": "A simple list containing PacBio data in either fasta or fastq formats with trimmed adapters. These are usually generated by contiging workflows and have tag \"trimmed_hifi\" associated with them.\n", @@ -181,11 +184,44 @@ "workflow_outputs": [] }, "6": { - "annotation": "Taxonomic lineage for the organism being assembled for Busco analysis.\n", + "annotation": "", "content_id": null, "errors": null, "id": 6, "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Database for Busco Lineage" + } + ], + "label": "Database for Busco Lineage", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 265.7339336519477, + "top": 639.7798327397703 + }, + "tool_id": null, + "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "b9c24106-80b7-46ba-9f50-1dcfc7d434d7", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "c7d6dfcd-5f5a-410e-b4cf-ce62dcbd7569" + } + ] + }, + "7": { + "annotation": "Taxonomic lineage for the organism being assembled for Busco analysis.\n", + "content_id": null, + "errors": null, + "id": 7, + "input_connections": {}, "inputs": [ { "description": "Taxonomic lineage for the organism being assembled for Busco analysis.\n", @@ -196,8 +232,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 216.70703125, - "top": 631.06640625 + "left": 294.03105732816533, + "top": 746.4774503653352 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", @@ -205,13 +241,19 @@ "type": "parameter_input", "uuid": "a489e27a-9a41-41e2-ab57-db2e855b1018", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "312c40bd-ea21-4624-842a-85f8369b8dfb" + } + ] }, - "7": { + "8": { "annotation": "", "content_id": null, "errors": null, - "id": 7, + "id": 8, "input_connections": {}, "inputs": [ { @@ -232,13 +274,19 @@ "type": "data_input", "uuid": "f53ab5b0-6b4d-43ea-8876-a1e2476fc7c6", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "ed6c5809-74a5-41e2-9efc-49af166df64c" + } + ] }, - "8": { + "9": { "annotation": "", "content_id": null, "errors": null, - "id": 8, + "id": 9, "input_connections": {}, "inputs": [ { @@ -259,13 +307,19 @@ "type": "parameter_input", "uuid": "2952f3e6-cc98-4cbe-ac46-32adb482ff3d", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "d52023b4-c747-4c66-82f6-5f017ee6413f" + } + ] }, - "9": { + "10": { "annotation": "", "content_id": null, "errors": null, - "id": 9, + "id": 10, "input_connections": {}, "inputs": [ { @@ -286,13 +340,19 @@ "type": "parameter_input", "uuid": "fd024c72-fe6c-4cd9-ac28-c8e86eaafc4f", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": 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"output_name": "integer_param" } }, @@ -818,22 +956,22 @@ } ] }, - "20": { + "23": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0", "errors": null, - "id": 20, + "id": 23, "input_connections": { "function_select|coverage": { - "id": 19, + "id": 22, "output_name": "pbcstat_cov" }, "function_select|cutoffs": { - "id": 19, + "id": 22, "output_name": "calcuts_cutoff" }, "function_select|input": { - "id": 14, + "id": 17, "output_name": "alignment_output" } }, @@ -884,14 +1022,14 @@ "when": null, "workflow_outputs": [] }, - "21": { + "24": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0", "errors": null, - "id": 21, + "id": 24, "input_connections": { "function_select|bed_input": { - "id": 20, + "id": 23, "output_name": "purge_dups_bed" }, "function_select|fasta_input": { @@ -966,14 +1104,14 @@ } ] }, - "22": { + "25": { "annotation": "", "content_id": "cat1", "errors": null, - 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{ + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "fbf99087e067", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"#\", \"replace_pattern\": \"Number of\", \"is_regex\": false, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "9.3+galaxy1", + "type": "tool", + "uuid": "94fb5ab8-0ebf-4302-992f-b8ca42b01780", + "when": null, + "workflow_outputs": [ + { + "label": "clean_stats", + "output_name": "outfile", + "uuid": "a022ab8b-306a-4035-8604-810d39f1bde7" } ] } @@ -3441,6 +3968,6 @@ "tags": [ "VGP_curated" ], - "uuid": "4818fdda-7a91-481a-a62f-ccab45a3c0f1", - "version": 2 + "uuid": "b5d0e4ae-3041-4cbe-9d0e-a1140e5469dd", + "version": 10 } \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/README.md b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/README.md index b2d6c9577..9aeae97b2 100644 --- a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/README.md +++ b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/README.md @@ -11,9 +11,11 @@ This workflow is the 6th workflow of the VGP pipeline. It is meant to be run aft 4. K-mer database [meryldb] (Generated by the k-mer profiling workflow) 5. Genomescope model parameters [txt] (Generated by the k-mer profiling workflow) 6. Estimated Genome Size [txt] -7. Name of first haplotype -8. Name of second haplotype -9. Lineage of you species for Busco Orthologs +7. Database for busco lineage (recommended: latest) +8. Lineage of your species for Busco Orthologs (recommended: vertebrata) +9. Name of first haplotype +10. Name of second haplotype + ## Outputs diff --git a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md index 10ed96a6a..788cbec76 100644 --- a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.7.1] 2024-08-13 + +- Expose Busco parameters : + - Lineage database + - Lineage + ## [0.7] 2024-07-24 ### Added diff --git a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b-tests.yml b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b-tests.yml index 473b556b5..b6e202663 100644 --- a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b-tests.yml +++ b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b-tests.yml @@ -29,6 +29,8 @@ location: https://zenodo.org/records/10632760/files/Trimmed_yeast_reads_sub1.fastq.gz?download=1 Name of un-altered assembly: Hap2 Name of purged assembly: Hap1 + Database for Busco Lineage: v5 + Lineage: vertebrata_odb10 outputs: Removed haplotigs: asserts: diff --git a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b.ga b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b.ga index 41128c4e8..f85038526 100644 --- a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b.ga +++ b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b.ga @@ -15,7 +15,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.7", + "release": "0.7.1", "name": "Purging-duplicates-one-haplotype-VGP6b ", "report": { "markdown": "\n# Workflow Execution Report\n\nTime workflow was invoked\n\n```galaxy\ninvocation_time()\n```\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Merqury results\n\nMerqury QV:\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_QV\")\n```\n\nMerqury completeness:\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_stats\")\n```\n\nMerqury plots:\n\nspectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-cn.fl\")\n```\n\n\nspectra-asm:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-asm.fl\")\n```\n\n\nhap1 spectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_01.spectra-cn.fl\")\n```\n\n\nhap2 spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_02.spectra-cn.fl\")\n```\n\n\n\n\n## BUSCO results (Vertebrata database)\n\nPurged Assembly\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco on Purged Primary assembly: summary image\")\n```\n\n\n## Assembly statistics\n\n\n```galaxy\nhistory_dataset_as_table(output=\"clean_stats\")\n```\n\n\n## Nx and Size plots\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Nx Plot\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Size Plot\")\n```\n\n\n\n## Current Workflow\n```galaxy\nworkflow_display()\n```\n" @@ -189,6 +189,60 @@ "errors": null, "id": 6, "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Database for Busco Lineage" + } + ], + "label": "Database for Busco Lineage", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 1705.6584960887728, + "top": 1674.0155168754275 + }, + "tool_id": null, + "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "1562a9b8-e3b5-473f-9f77-e09693d1a98f", + "when": null, + "workflow_outputs": [] + }, + "7": { + "annotation": "Taxonomic lineage for the organism being assembled for Busco analysis", + "content_id": null, + "errors": null, + "id": 7, + "input_connections": {}, + "inputs": [ + { + "description": "Taxonomic lineage for the organism being assembled for Busco analysis", + "name": "Lineage" + } + ], + "label": "Lineage", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 1718.7343010232019, + "top": 1810.02258129551 + }, + "tool_id": null, + "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "f95d611e-99bd-43a3-8455-b87df2071d01", + "when": null, + "workflow_outputs": [] + }, + "8": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 8, + "input_connections": {}, "inputs": [ { "description": "", @@ -210,11 +264,11 @@ "when": null, "workflow_outputs": [] }, - 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"id": 23, + "id": 25, "input_connections": { "infile": { - "id": 22, + "id": 24, "output_name": "purge_dups_bed" } }, @@ -1407,14 +1461,14 @@ "when": null, "workflow_outputs": [] }, - "24": { + "26": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0", "errors": null, - "id": 24, + "id": 26, "input_connections": { "function_select|bed_input": { - "id": 23, + "id": 25, "output_name": "output" }, "function_select|fasta_input": { @@ -1501,14 +1555,14 @@ } ] }, - "25": { + "27": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4", "errors": null, - "id": 25, + "id": 27, "input_connections": { "mode|assembly_options|assembly_01": { - "id": 24, + "id": 26, "output_name": "get_seqs_purged" }, "mode|assembly_options|assembly_02": { @@ -1635,14 +1689,14 @@ } ] }, - "26": { + "28": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 26, + "id": 28, "input_connections": { "input_file": { - "id": 24, + "id": 26, "output_name": "get_seqs_purged" } }, @@ -1687,15 +1741,23 @@ "when": null, "workflow_outputs": [] }, - "27": { + "29": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0", "errors": null, - "id": 27, + "id": 29, "input_connections": { "input": { - "id": 24, + "id": 26, "output_name": "get_seqs_purged" + }, + "lineage_conditional|cached_db": { + "id": 6, + "output_name": "output" + }, + "lineage|lineage_dataset": { + "id": 7, + "output_name": "output" } }, "inputs": [], @@ -1771,7 +1833,7 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": \"vertebrata_odb10\"}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"cached\", \"__current_case__\": 0, \"cached_db\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "5.5.0+galaxy0", "type": "tool", "uuid": "73b62ef3-0002-418e-9f10-22076c1e48f3", @@ -1789,14 +1851,14 @@ } ] }, - "28": { + "30": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 28, + "id": 30, "input_connections": { "input_file": { - "id": 24, + "id": 26, "output_name": "get_seqs_purged" } }, @@ -1849,18 +1911,18 @@ } ] }, - "29": { + "31": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 29, + "id": 31, "input_connections": { "input_file": { - "id": 24, + "id": 26, "output_name": "get_seqs_purged" }, "mode_condition|statistics_condition|expected_genomesize": { - "id": 12, + "id": 14, "output_name": "integer_param" } }, @@ -1906,14 +1968,14 @@ } ] }, - "30": { + "32": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 30, + "id": 32, "input_connections": { "input": { - "id": 25, + "id": 27, "output_name": "qv_files" } }, @@ -1951,14 +2013,14 @@ } ] }, - "31": { + "33": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 31, + "id": 33, "input_connections": { "input": { - "id": 25, + "id": 27, "output_name": "png_files" } }, @@ -2003,14 +2065,14 @@ } ] }, - "32": { + "34": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 32, + "id": 34, "input_connections": { "input": { - "id": 25, + "id": 27, "output_name": "png_files" } }, @@ -2055,14 +2117,14 @@ } ] }, - "33": { + "35": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 33, + "id": 35, "input_connections": { "input": { - "id": 25, + "id": 27, "output_name": "png_files" } }, @@ -2107,14 +2169,14 @@ } ] }, - "34": { + "36": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 34, + "id": 36, "input_connections": { "input": { - "id": 25, + "id": 27, "output_name": "stats_files" } }, @@ -2152,14 +2214,14 @@ } ] }, - "35": { + "37": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 35, + "id": 37, "input_connections": { "input": { - "id": 25, + "id": 27, "output_name": "png_files" } }, @@ -2204,12 +2266,12 @@ } ] }, - "36": { + "38": { "annotation": "", - "id": 36, + "id": 38, "input_connections": { "gfa_stats": { - "id": 26, + "id": 28, "input_subworkflow_step_id": 0, "output_name": "stats" } @@ -2581,14 +2643,14 @@ "when": null, "workflow_outputs": [] }, - "37": { + "39": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "errors": null, - "id": 37, + "id": 39, "input_connections": { "infile": { - "id": 29, + "id": 31, "output_name": "stats" } }, @@ -2626,27 +2688,27 @@ "when": null, "workflow_outputs": [] }, - "38": { + "40": { "annotation": "", - "id": 38, + "id": 40, "input_connections": { "Alternate data": { - "id": 16, + "id": 18, "input_subworkflow_step_id": 1, "output_name": "gfastats data for plotting" }, "Name of alternate assembly": { - "id": 7, + "id": 9, "input_subworkflow_step_id": 3, "output_name": "output" }, "Name of primary assembly": { - "id": 6, + "id": 8, "input_subworkflow_step_id": 2, "output_name": "output" }, "Primary data": { - "id": 36, + "id": 38, "input_subworkflow_step_id": 0, "output_name": "gfastats data for plotting" } @@ -3164,18 +3226,18 @@ } ] }, - "39": { + "41": { "annotation": "", "content_id": "join1", "errors": null, - "id": 39, + "id": 41, "input_connections": { "input1": { - "id": 37, + "id": 39, "output_name": "outfile" }, "input2": { - "id": 20, + "id": 22, "output_name": "outfile" } }, @@ -3207,14 +3269,14 @@ "when": null, "workflow_outputs": [] }, - "40": { + "42": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1", "errors": null, - "id": 40, + "id": 42, "input_connections": { "input": { - "id": 39, + "id": 41, "output_name": "out_file1" } }, @@ -3267,14 +3329,14 @@ } ] }, - "41": { + "43": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "errors": null, - "id": 41, + "id": 43, "input_connections": { "infile": { - "id": 40, + "id": 42, "output_name": "output" } }, @@ -3322,6 +3384,6 @@ "tags": [ "VGP_curated" ], - "uuid": "7d187438-e7da-494b-ba1f-993da4174e79", - "version": 14 + "uuid": "727b2b8c-3ff1-4736-952d-b2c215c0faa1", + "version": 1 } \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/README.md b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/README.md index 3c58d2ee4..ad3b26735 100644 --- a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/README.md +++ b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/README.md @@ -6,13 +6,15 @@ This workflow is the 6th workflow of the VGP pipeline. It is meant to be run aft ## Inputs 1. Genomescope model parameters [txt] (Generated by the k-mer profiling workflow) -1. Hifi long reads - trimmed [fastq] (Generated by Cutadapt in the contigging workflow) -2. Assembly to purge (e.g. hap1) [fasta] (Generated by the contigging workflow) -3. K-mer database [meryldb] (Generated by the k-mer profiling workflow) -4. Estimated Genome Size [txt] +2. Hifi long reads - trimmed [fastq] (Generated by Cutadapt in the contigging workflow) +3. Assembly to purge (e.g. hap1) [fasta] (Generated by the contigging workflow) +4. K-mer database [meryldb] (Generated by the k-mer profiling workflow) 5. Assembly to leave alone (used for merqury statistics) (e.g. hap2) [fasta] (Generated by the contigging workflow) -6. Name of un-altered assembly -7. Name of purged assembly +6. Estimated Genome Size [txt] +7. Database for busco lineage (recommended: latest) +8. Busco lineage (recommended: vertebrata) +9. Name of un-altered assembly +10. Name of purged assembly ## Outputs diff --git a/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/CHANGELOG.md b/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/CHANGELOG.md index 8a3d28224..c97a841c8 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/CHANGELOG.md @@ -1,5 +1,9 @@ # Changelog +## [0.1.4] 2024-08-13 + +- Addition of workflow report + ## [0.1.3] 2024-04-01 ### Automatic update diff --git a/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/Scaffolding-BioNano-VGP7.ga b/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/Scaffolding-BioNano-VGP7.ga index cd3691f4b..326a74a51 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/Scaffolding-BioNano-VGP7.ga +++ b/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/Scaffolding-BioNano-VGP7.ga @@ -1,6 +1,7 @@ { "a_galaxy_workflow": "true", "annotation": "", + "comments": [], "creator": [ { "class": "Organization", @@ -14,8 +15,11 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.1.3", + "release": "0.1.4", "name": "Scaffolding-BioNano-VGP7", + "report": { + "markdown": "\n# Workflow Execution Report\n\n## Invocation time\n```galaxy\ninvocation_time()\n```\n\n## Assembly statistics\n\n```galaxy\nhistory_dataset_as_table(output=\"clean_stats\")\n```\n\n## Size plot\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Size Plot\")\n```\n\n\n## Nx plot\n```galaxy\nhistory_dataset_as_image(output=\"Nx Plot\")\n```\n\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" + }, "steps": { "0": { "annotation": "", @@ -123,13 +127,7 @@ "type": "data_input", "uuid": "404dfe4f-8590-486e-b632-a0564010e213", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "5957fae6-c14a-464a-aedb-0695d68d69dd" - } - ] + "workflow_outputs": [] }, "4": { "annotation": "", @@ -181,12 +179,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -352,12 +345,7 @@ "output_name": "ngs_contigs_scaffold_agp" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -417,12 +405,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -562,7 +545,58 @@ }, "11": { "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", + "errors": null, "id": 11, + "input_connections": { + "infile": { + "id": 9, + "output_name": "stats" + } + }, + "inputs": [], + "label": null, + "name": "Replace", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 2430.427837638421, + "top": 236.31263207430692 + }, + "post_job_actions": { + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "fbf99087e067", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"#\", \"replace_pattern\": \"Number of\", \"is_regex\": false, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "9.3+galaxy1", + "type": "tool", + "uuid": "292e7cba-fa66-4f7e-935d-504d64a304cc", + "when": null, + "workflow_outputs": [ + { + "label": "clean_stats", + "output_name": "outfile", + "uuid": "4a0bdf73-d0f9-4c54-9c82-9a63e19e4695" + } + ] + }, + "12": { + "annotation": "", + "id": 12, "input_connections": { "gfa_stats": { "id": 10, @@ -922,7 +956,7 @@ ] } }, - "tags": "", + "tags": [], "uuid": "0d43f853-69ee-4f89-9a1d-50cfa45ec0fd" }, "tool_id": null, @@ -931,14 +965,14 @@ "when": null, "workflow_outputs": [] }, - "12": { + "13": { "annotation": "", "content_id": "Cut1", "errors": null, - "id": 12, + "id": 13, "input_connections": { "input": { - "id": 11, + "id": 12, "output_name": "gfastats data for plotting" } }, @@ -970,14 +1004,14 @@ "when": null, "workflow_outputs": [] }, - "13": { + "14": { "annotation": "", "content_id": "Cut1", "errors": null, - "id": 13, + "id": 14, "input_connections": { "input": { - "id": 11, + "id": 12, "output_name": "gfastats data for plotting" } }, @@ -1009,14 +1043,14 @@ "when": null, "workflow_outputs": [] }, - "14": { + "15": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1", "errors": null, - "id": 14, + "id": 15, "input_connections": { "input1": { - "id": 12, + "id": 13, "output_name": "out_file1" } }, @@ -1062,14 +1096,14 @@ } ] }, - "15": { + "16": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1", "errors": null, - "id": 15, + "id": 16, "input_connections": { "input1": { - "id": 13, + "id": 14, "output_name": "out_file1" } }, @@ -1119,6 +1153,6 @@ "tags": [ "VGP_curated" ], - "uuid": "0c8b790c-4dce-4e9b-b942-da71a9e9b27e", - "version": 5 + "uuid": "9fd3c0de-a497-47dc-96e3-0f3e1998173d", + "version": 6 } \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md index bda23d114..d71b86cda 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md @@ -1,5 +1,19 @@ # Changelog + +## [0.2.8] 2024-09-12 + +- Add suffix to the scaffold names corresponding to the haplotype being assembled + +## [0.2.7] 2024-08-13 + +- Expose Busco lineage database parameter + +## [0.2.6] 2024-08-05 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy2` + ## [0.2.5] 2024-07-31 - Addition of Workflow report diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/README.md b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/README.md index 16413b667..e497e5704 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/README.md +++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/README.md @@ -10,10 +10,14 @@ Example of trajectory : ## Inputs 1. Scaffolded assembly [fasta] -2. Concatenated HiC forward reads [fastq] -3. Concatenated HiC reverse reads [fastq] -4. Restriction enzyme sequence [txt] -5. Estimated genome size [txt] +2. Database for busco lineage (recommended: latest) +3. Busco lineage (recommended: vertebrata) +4. Concatenated HiC forward reads [fastq] +5. Concatenated HiC reverse reads [fastq] +6. Restriction enzyme sequence (recommended for VGP data: Arima Hi-C 2.0) +7. Estimated genome size [txt] +8. Haplotype name + ### Outputs diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8-tests.yml b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8-tests.yml index 638d990be..a73013131 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8-tests.yml +++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8-tests.yml @@ -16,8 +16,10 @@ class: File location: https://zenodo.org/records/10037496/files/Estimated%20genome%20size%20-%20Parameter%20File.txt?download=1 filetype: txt + Database for Busco Lineage: v5 Lineage: vertebrata_odb10 Restriction enzymes: arima2 + Haplotype: hap1 outputs: "Reconciliated Scaffolds: gfa": asserts: @@ -27,6 +29,8 @@ asserts: has_n_lines: n: 168 + has_text: + text: "scaffold_53.hap1" Busco Summary: asserts: has_text: diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga index 13a9a4eb9..499b03b32 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga +++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga @@ -15,8 +15,8 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.2.5", - "name": "Scaffolding-HiC-VGP8", + "release": "0.2.8", + "name": "Scaffolding with Hi-C data VGP8", "report": { "markdown": "# Workflow Execution Report\n\nTime workflow was invoked\n\n```galaxy\ninvocation_time()\n```\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n\n## BUSCO results (Vertebrata database)\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary image\")\n```\n\n\n## Assembly statistics\n\n\n```galaxy\nhistory_dataset_as_table(output=\"clean_stats\")\n```\n\n\n## Nx and Size plots\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Nx Plot\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Size Plot\")\n```\n\n## PretextMap\n\n### Before Scaffolding\n\n\r\n```galaxy\nhistory_dataset_as_image(output=\"Pretext Map Before HiC scaffolding\")\n```\r\n\n\n### After Scaffolding\r\n```galaxy\nhistory_dataset_as_image(output=\"Pretext Map After HiC scaffolding\")\n```\r\n\n\n\n\n## Current Workflow\n```galaxy\nworkflow_display()\n```\n" }, @@ -38,7 +38,7 @@ "outputs": [], "position": { "left": 0, - "top": 163.55078125 + "top": 220.18215513867335 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -54,6 +54,39 @@ "errors": null, "id": 1, "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Haplotype" + } + ], + "label": "Haplotype", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 10.342401705473666, + "top": 303.58456411376267 + }, + "tool_id": null, + "tool_state": "{\"restrictions\": [\"hap1\", \"hap2\", \"mat\", \"pat\", \"pri\", \"alt\"], \"parameter_type\": \"text\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "3495a63c-bcd5-45fa-b327-ed7ec0234e78", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "1c4419fd-2eca-4464-9a67-4d693379981b" + } + ] + }, + "2": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, "inputs": [ { "description": "", @@ -65,7 +98,7 @@ "outputs": [], "position": { "left": 2.48046875, - "top": 320.09375 + "top": 376.72512388867335 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": \"\"}", @@ -77,15 +110,48 @@ { "label": null, "output_name": "output", - "uuid": "bd94bf34-0ed3-42f3-888d-36a56e74ff5b" + "uuid": "8886e85a-6c79-49f0-8291-357583692bec" } ] }, - "2": { + "3": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 3, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Database for Busco Lineage" + } + ], + "label": "Database for Busco Lineage", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 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null, - "id": 22, + "id": 26, "input_connections": { "fastq_input|fastq_input1": { - "id": 4, + "id": 6, "output_name": "output" }, "reference_source|ref_file": { - "id": 18, + "id": 22, "output_name": "output" } }, @@ -1043,7 +1191,7 @@ ], "position": { "left": 3497.922433120587, - "top": 828.171875 + "top": 884.8032488886734 }, "post_job_actions": { "HideDatasetActionbam_output": { @@ -1066,18 +1214,22 @@ "when": null, "workflow_outputs": [] }, - "23": { + "27": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0", "errors": null, - "id": 23, + "id": 27, "input_connections": { "input": { - "id": 18, + "id": 22, + "output_name": "output" + }, + "lineage_conditional|cached_db": { + "id": 3, "output_name": "output" }, "lineage|lineage_dataset": { - "id": 2, + "id": 4, "output_name": "output" } }, @@ -1103,8 +1255,8 @@ } ], "position": { - "left": 3784.714433375001, - "top": 276.07421875 + "left": 3784.7033413689933, + "top": 301.3947338398648 }, 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"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "errors": null, - "id": 24, + "id": 28, "input_connections": { "infile": { - "id": 19, + "id": 23, "output_name": "stats" } }, @@ -1183,7 +1335,7 @@ ], "position": { "left": 4038.9643691913197, - "top": 1953.52949196313 + "top": 2010.1608658518035 }, "post_job_actions": { "HideDatasetActionoutfile": { @@ -1194,12 +1346,12 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"#\", \"replace_pattern\": \"Number of\", \"is_regex\": false, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"#\", \"replace_pattern\": \"Number of\", \"is_regex\": false, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "9.3+galaxy1", "type": "tool", "uuid": "4b0a88b6-47cc-4381-949c-fc18a99799ac", @@ -1212,12 +1364,12 @@ } ] }, - "25": { + "29": { "annotation": "", - "id": 25, + "id": 29, "input_connections": { "gfa_stats": { - "id": 20, + "id": 24, "input_subworkflow_step_id": 0, "output_name": "stats" } @@ -1228,7 +1380,7 @@ "outputs": [], "position": { "left": 4372.234933120587, - "top": 1677.609375 + "top": 1734.2407488886734 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -1336,7 +1488,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1575,7 +1727,7 @@ } }, "tags": [], - "uuid": "0a29c4ba-6eeb-4812-85dd-4c5a5682d8cf" + "uuid": "b30c8dd0-24e7-4e74-ad9b-5fefd27893fa" }, "tool_id": null, "type": "subworkflow", @@ -1583,18 +1735,18 @@ "when": null, "workflow_outputs": [] }, - "26": { + "30": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1", "errors": null, - "id": 26, + "id": 30, "input_connections": { "forward": { - "id": 21, + "id": 25, "output_name": "bam_output" }, "reverse": { - "id": 22, + "id": 26, "output_name": "bam_output" } }, @@ -1609,7 +1761,7 @@ ], "position": { "left": 3801.906808120587, - "top": 827.390625 + "top": 884.0219988886734 }, "post_job_actions": { "TagDatasetActionoutfile": { @@ -1634,14 +1786,14 @@ "when": null, "workflow_outputs": [] }, - "27": { + "31": { "annotation": "", "content_id": "Cut1", "errors": null, - "id": 27, + "id": 31, "input_connections": { "input": { - "id": 25, + "id": 29, "output_name": "gfastats data for plotting" } }, @@ -1656,7 +1808,7 @@ ], "position": { "left": 4935.641183120587, - "top": 1404.421875 + "top": 1461.0532488886734 }, "post_job_actions": {}, "tool_id": "Cut1", @@ -1667,14 +1819,14 @@ "when": null, "workflow_outputs": [] }, - "28": { + "32": { "annotation": "", "content_id": "Cut1", "errors": null, - "id": 28, + "id": 32, "input_connections": { "input": { - "id": 25, + "id": 29, "output_name": "gfastats data for plotting" } }, @@ -1689,7 +1841,7 @@ ], "position": { "left": 4937.672433120587, - "top": 1545.40625 + "top": 1602.0376238886734 }, "post_job_actions": { "HideDatasetActionout_file1": { @@ -1706,14 +1858,14 @@ "when": null, "workflow_outputs": [] }, - "29": { + "33": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1", "errors": null, - "id": 29, + "id": 33, "input_connections": { "input": { - "id": 26, + "id": 30, "output_name": "outfile" } }, @@ -1728,7 +1880,7 @@ ], "position": { "left": 4140.766183120587, - "top": 961.375 + "top": 1018.0063738886734 }, "post_job_actions": { "TagDatasetActionpretext_map_out": { @@ -1753,14 +1905,14 @@ "when": null, "workflow_outputs": [] }, - "30": { + "34": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0", "errors": null, - "id": 30, + "id": 34, "input_connections": { "input": { - "id": 26, + "id": 30, "output_name": "outfile" } }, @@ -1775,7 +1927,7 @@ ], "position": { "left": 4282.953683120587, - "top": 721.03125 + "top": 777.6626238886734 }, "post_job_actions": { "HideDatasetActionoutput": { @@ -1798,14 +1950,14 @@ "when": null, "workflow_outputs": [] }, - "31": { + "35": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1", "errors": null, - "id": 31, + "id": 35, "input_connections": { "input1": { - "id": 27, + "id": 31, "output_name": "out_file1" } }, @@ -1820,7 +1972,7 @@ ], "position": { "left": 5215.016183120587, - "top": 1327.078125 + "top": 1383.7094988886734 }, "post_job_actions": { "RenameDatasetActionoutput1": { @@ -1858,14 +2010,14 @@ } ] }, - "32": { + "36": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1", "errors": null, - "id": 32, + "id": 36, "input_connections": { "input1": { - "id": 28, + "id": 32, "output_name": "out_file1" } }, @@ -1880,7 +2032,7 @@ ], "position": { "left": 5206.734933120587, - "top": 1561.296875 + "top": 1617.9282488886734 }, "post_job_actions": { "RenameDatasetActionoutput1": { @@ -1918,14 +2070,14 @@ } ] }, - "33": { + "37": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2", "errors": null, - "id": 33, + "id": 37, "input_connections": { "input": { - "id": 29, + "id": 33, "output_name": "pretext_map_out" } }, @@ -1940,7 +2092,7 @@ ], "position": { "left": 4509.1334844570965, - "top": 1064.8994221213547 + "top": 1121.530796010028 }, "post_job_actions": { "HideDatasetActionpretext_snap_out": { @@ -1970,14 +2122,14 @@ "when": null, "workflow_outputs": [] }, - "34": { + "38": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1", "errors": null, - "id": 34, + "id": 38, "input_connections": { "infile": { - "id": 30, + "id": 34, "output_name": "output" } }, @@ -1992,7 +2144,7 @@ ], "position": { "left": 4596.258316145335, - "top": 390.1009386788954 + "top": 446.7323125675687 }, "post_job_actions": { "TagDatasetActionoutfile": { @@ -2005,7 +2157,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -2017,14 +2169,14 @@ "when": null, "workflow_outputs": [] }, - "35": { + "39": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 35, + "id": 39, "input_connections": { "input": { - "id": 33, + "id": 37, "output_name": "pretext_snap_out" } }, @@ -2039,7 +2191,7 @@ ], "position": { "left": 4773.453683120587, - "top": 1125.96875 + "top": 1182.6001238886734 }, "post_job_actions": { "TagDatasetActionoutput": { @@ -2068,6 +2220,6 @@ "tags": [ "VGP_curated" ], - "uuid": "88cb8c3c-791b-4ab8-b982-4811f6f94630", - "version": 5 + "uuid": "dbe64df1-13fc-49fa-8a14-ead72f9d7ea1", + "version": 7 } \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md index 0b3001964..02da3755e 100644 --- a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [0.1.7] 2024-08-05 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0.1+galaxy0` + ## [0.1.6] 2024-07-12 - Add workflow report diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1-tests.yml b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1-tests.yml index 7c28a630e..3f79a85b4 100644 --- a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1-tests.yml +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1-tests.yml @@ -12,22 +12,18 @@ Ploidy: 1 outputs: GenomeScope linear plot: - class: File file: test-data/GenomeScope_Linear_plot.png compare: sim_size delta: 10000 GenomeScope log plot: - class: File file: test-data/GenomeScope_Log_plot.png compare: sim_size delta: 10000 GenomeScope transformed linear plot: - class: File file: test-data/GenomeScope_Transformed_linear_plot.png compare: sim_size delta: 10000 GenomeScope transformed log plot: - class: File file: test-data/GenomeScope_Transformed_log_plot.png compare: sim_size delta: 10000 diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga index b3a112c3b..3e5142b9b 100644 --- a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga @@ -15,7 +15,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release":"0.1.6", + "release": "0.1.7", "name": "kmer-profiling-hifi-VGP1", "report": { "markdown": "\n# Workflow Execution Report\n\n\n```galaxy\ninvocation_time()\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope linear plot\")\n```\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope log plot\")\n```\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope transformed linear plot\")\n```\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope transformed log plot\")\n```\n\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" @@ -251,7 +251,7 @@ }, "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0.1+galaxy0", "errors": null, "id": 6, "input_connections": { @@ -356,15 +356,15 @@ "output_name": "transformed_log_plot" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "01210c4e9144", + "changeset_revision": "460fad600dce", "name": "genomescope", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"advanced_options\": {\"topology\": null, \"initial_repetitiveness\": null, \"initial_heterozygosities\": \"\", \"transform_exp\": null, \"testing\": true, \"true_params\": \"\", \"trace_flag\": false, \"num_rounds\": null}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"kmer_length\": {\"__class__\": \"ConnectedValue\"}, \"lambda\": null, \"max_kmercov\": null, \"output_options\": {\"output_files\": [\"model_output\", \"summary_output\"], \"no_unique_sequence\": false}, \"ploidy\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.0+galaxy2", + "tool_version": "2.0.1+galaxy0", "type": "tool", "uuid": "955de351-ef19-42dc-89d7-ca213994515a", "when": null, @@ -408,4 +408,4 @@ ], "uuid": "0808b15a-7e3e-4b06-b804-f3d2cc73981a", "version": 2 -} \ No newline at end of file +} diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/CHANGELOG.md b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/CHANGELOG.md index 06a53f900..9fd63f4a8 100644 --- a/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [0.1.4] 2024-08-05 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0.1+galaxy0` + ## [0.1.3] 2023-11-20 - Fix author in dockstore diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2-tests.yml b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2-tests.yml index 1d9044cfb..43888eb13 100644 --- a/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2-tests.yml +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2-tests.yml @@ -36,17 +36,14 @@ Ploidy: 1 outputs: GenomeScope linear plot (maternal): - class: File file: test-data/GenomeScope_Linear_plot_maternal.png compare: sim_size delta: 15000 GenomeScope linear plot (paternal): - class: File file: test-data/GenomeScope_Linear_plot_paternal.png compare: sim_size delta: 15000 GenomeScope linear plot (child): - class: File file: test-data/GenomeScope_Linear_plot_child.png compare: sim_size delta: 15000 diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2.ga b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2.ga index 11c7afc43..f374f3a93 100644 --- a/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2.ga +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2.ga @@ -14,7 +14,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.1.3", + "release": "0.1.4", "name": "kmer-profiling-hifi-trio-VGP2", "steps": { "0": { @@ -442,7 +442,7 @@ }, "9": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0.1+galaxy0", "errors": null, "id": 9, "input_connections": { @@ -547,15 +547,15 @@ "output_name": "transformed_log_plot" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "01210c4e9144", + "changeset_revision": "460fad600dce", "name": "genomescope", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"advanced_options\": {\"topology\": null, \"initial_repetitiveness\": null, \"initial_heterozygosities\": \"\", \"transform_exp\": null, \"testing\": true, \"true_params\": \"\", \"trace_flag\": false, \"num_rounds\": null}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"kmer_length\": {\"__class__\": \"ConnectedValue\"}, \"lambda\": null, \"max_kmercov\": null, \"output_options\": {\"output_files\": [\"model_output\", \"summary_output\"], \"no_unique_sequence\": false}, \"ploidy\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.0+galaxy2", + "tool_version": "2.0.1+galaxy0", "type": "tool", "uuid": "12e75ec0-5722-4ad7-b333-636c3c9ad9c8", "when": null, @@ -729,7 +729,7 @@ }, "13": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0.1+galaxy0", "errors": null, "id": 13, "input_connections": { @@ -833,15 +833,15 @@ "output_name": "transformed_log_plot" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "01210c4e9144", + "changeset_revision": "460fad600dce", "name": "genomescope", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"advanced_options\": {\"topology\": null, \"initial_repetitiveness\": null, \"initial_heterozygosities\": \"\", \"transform_exp\": null, \"testing\": false, \"true_params\": \"\", \"trace_flag\": false, \"num_rounds\": null}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"kmer_length\": {\"__class__\": \"ConnectedValue\"}, \"lambda\": null, \"max_kmercov\": null, \"output_options\": {\"output_files\": [\"model_output\", \"summary_output\"], \"no_unique_sequence\": false}, \"ploidy\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.0+galaxy2", + "tool_version": "2.0.1+galaxy0", "type": "tool", "uuid": "c65bd0f5-d8d5-4d1d-81bf-6d05458bc160", "when": null, @@ -870,7 +870,7 @@ }, "14": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0.1+galaxy0", "errors": null, "id": 14, "input_connections": { @@ -974,15 +974,15 @@ "output_name": "transformed_log_plot" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "01210c4e9144", + "changeset_revision": "460fad600dce", "name": "genomescope", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"advanced_options\": {\"topology\": null, \"initial_repetitiveness\": null, \"initial_heterozygosities\": \"\", \"transform_exp\": null, \"testing\": false, \"true_params\": \"\", \"trace_flag\": false, \"num_rounds\": null}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"kmer_length\": {\"__class__\": \"ConnectedValue\"}, \"lambda\": null, \"max_kmercov\": null, \"output_options\": {\"output_files\": [\"model_output\", \"summary_output\"], \"no_unique_sequence\": false}, \"ploidy\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.0+galaxy2", + "tool_version": "2.0.1+galaxy0", "type": "tool", "uuid": "87497ba1-5c23-4852-9e2f-0bd78dc86753", "when": null, @@ -1016,4 +1016,4 @@ ], "uuid": "af01815b-5b66-4578-ade7-6e2caed0c19a", "version": 9 -} \ No newline at end of file +} diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.dockstore.yml b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.dockstore.yml new file mode 100644 index 000000000..2031035d2 --- /dev/null +++ b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.dockstore.yml @@ -0,0 +1,25 @@ +version: 1.2 +workflows: +- name: QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis + subclass: Galaxy + publish: true + primaryDescriptorPath: /QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga + testParameterFiles: + - /QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml + authors: + - name: Debjyoti Ghosh + orcid: 0009-0008-1496-1677 + - name: "Helmholtz-Zentrum für Umweltforschung - UFZ" + address: "Permoserstraße 15, 04318 Leipzig" + +- name: QIIME2-VI-diversity-metrics-and-estimations + subclass: Galaxy + publish: true + primaryDescriptorPath: /QIIME2-VI-diversity-metrics-and-estimations.ga + testParameterFiles: + - /QIIME2-VI-diversity-metrics-and-estimations-tests.yml + authors: + - name: Debjyoti Ghosh + orcid: 0009-0008-1496-1677 + - name: "Helmholtz-Zentrum für Umweltforschung - UFZ" + address: "Permoserstraße 15, 04318 Leipzig" \ No newline at end of file diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.workflowhub.yml b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.workflowhub.yml new file mode 100644 index 000000000..2a1023efd --- /dev/null +++ b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.workflowhub.yml @@ -0,0 +1,5 @@ +version: '0.1' +registries: +- url: https://workflowhub.eu + project: iwc + workflow: qiime2/main diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/CHANGELOG.md b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/CHANGELOG.md new file mode 100644 index 000000000..7df9c9552 --- /dev/null +++ b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/CHANGELOG.md @@ -0,0 +1,4 @@ +# Changelog + +## [0.1] 2024-06-22 +First release. \ No newline at end of file diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml new file mode 100644 index 000000000..b5cf8d512 --- /dev/null +++ b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml @@ -0,0 +1,108 @@ +- doc: Test outline for QIIME2-III:-Phylogenetic-tree-for-diversity-analysis + job: + Metadata: + class: File + location: https://data.qiime2.org/2024.2/tutorials/pd-mice/sample_metadata.tsv + filetype: tabular + Representative sequences: + class: File + location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/dada2_rep_set.qza + filetype: qza + Feature table: + class: File + location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/dada2_table.qza + filetype: qza + Minimum depth: 1 + Maximum depth: 2019 + Taxonomic classifier: + class: File + location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/gg-13-8-99-515-806-nb-classifier.qza + filetype: qza + SEPP fragment insertion reference: + class: File + location: https://data.qiime2.org/2024.2/common/sepp-refs-gg-13-8.qza + filetype: qza + outputs: + Rooted tree: + ftype: qza + asserts: + - has_size: + min: 2M + max: 3M + - has_archive_member: + path: "^[^/]*/data/tree.nwk" + n: 1 + asserts: + - has_text_matching: + expression: "k__Bacteria" + - has_archive_member: + path: "^[^/]*/metadata.yaml" + n: 1 + asserts: + - has_line: + line: "type: Phylogeny[Rooted]" + - has_line: + line: "format: NewickDirectoryFormat" + + Rarefaction curve: + ftype: qzv + asserts: + - has_size: + min: 400k + max: 500k + - has_archive_member: + path: "^[^/]*/data/index.html" + n: 1 + # data per measure + - has_archive_member: + path: "^[^/]*/data/.*\\.csv" + n: 3 + # data for each measure and metadata variable (*7) + - has_archive_member: + path: "^[^/]*/data/.*\\.jsonp" + n: 21 + + Taxonomy classification: + ftype: qza + asserts: + - has_size: + min: 70k + max: 80k + - has_archive_member: + path: "^[^/]*/metadata.yaml" + n: 1 + asserts: + - has_line: + line: "type: FeatureData[Taxonomy]" + - has_line: + line: "format: TSVTaxonomyDirectoryFormat" + - has_archive_member: + path: "^[^/]*/data/taxonomy.tsv" + n: 1 + asserts: + - has_n_lines: + n: 288 + Taxa barplot: + ftype: qzv + asserts: + - has_size: + min: 400k + max: 500k + - has_archive_member: + path: "^[^/]*/data/.*\\.csv" + n: 7 + - has_archive_member: + path: "^[^/]*/data/.*\\.jsonp" + n: 7 + Taxonomy classification table: + ftype: qza + asserts: + - has_size: + min: 1M + max: 2M + - has_archive_member: + path: "^[^/]*/data/metadata.tsv" + n: 1 + asserts: + - has_n_lines: + n: 289 \ No newline at end of file diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga new file mode 100644 index 000000000..19b3f61c9 --- /dev/null +++ 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filetype: qiime2.tabular + Feature table: + class: File + location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/dada2_table.qza + filetype: qza + Rooted tree: + class: File + location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/tree.qza + filetype: qza + Sampling depth: '2000' + Target metadata parameter (for beta diversity): cage_id + outputs: + Alpha diversity - Pielou's evenness: + ftype: qzv + asserts: + - has_size: + min: 300k + max: 400k + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.csv" + n: 6 + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.jsonp" + n: 6 + Alpha diversity - Shannon's diversity index: + ftype: qzv + asserts: + - has_size: + min: 300k + max: 400k + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.csv" + n: 6 + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.jsonp" + n: 6 + Alpha diversity - Observed features: + ftype: qzv + asserts: + - has_size: + min: 300k + max: 400k + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.csv" + n: 6 + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.jsonp" + n: 6 + Beta diversity - Bray-Curtis distance metrics: + ftype: qzv + asserts: + - has_size: + min: 400k + max: 500k + - has_archive_member: + path: "^[^/]*/data/raw_data\\.tsv" + n: 1 + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.png" + n: 6 + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.pdf" + n: 6 + Beta diversity - Jaccard distance metrics: + ftype: qzv + asserts: + - has_size: + min: 400k + max: 500k + - has_archive_member: + path: "^[^/]*/data/raw_data\\.tsv" + n: 1 + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.png" + n: 6 + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.pdf" + n: 6 + Beta diversity - weighted UniFrac distance metrics: + ftype: qzv + asserts: + - has_size: + min: 400k + max: 500k + - has_archive_member: + path: "^[^/]*/data/raw_data\\.tsv" + n: 1 + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.png" + n: 6 + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.pdf" + n: 6 + Emperor plot collection: + element_tests: + 'unweighted_unifrac': + ftype: qzv + 'weighted_unifrac': + ftype: qzv + 'jaccard': + ftype: qzv + 'bray_curtis': + ftype: qzv + Distance matrix collection: + element_tests: + 'unweighted_unifrac': + ftype: qzv + 'weighted_unifrac': + ftype: qzv + 'jaccard': + ftype: qzv + 'bray_curtis': + ftype: qzv + PCoA collection: + element_tests: + 'unweighted_unifrac': + ftype: qzv + 'weighted_unifrac': + ftype: qzv + 'jaccard': + ftype: qzv + 'bray_curtis': + ftype: qzv + Richness and evenness collection: + element_tests: + 'rarefied_table': + ftype: qzv + 'faith_pd_vector': + ftype: qzv + 'observed_features_vector': + ftype: qzv + 'shannon_vector': + ftype: qzv + 'eveness_vector': + ftype: qzv \ No newline at end of file diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-VI-diversity-metrics-and-estimations.ga b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-VI-diversity-metrics-and-estimations.ga new file mode 100644 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1788.2942298465593, + "top": 1104.9898983924463 + }, + "post_job_actions": { + "RenameDatasetActionoutput": { + "action_arguments": { + "newname": "collection_richness_evenness" + }, + "action_type": "RenameDatasetAction", + "output_name": "output" + } + }, + "tool_id": "__BUILD_LIST__", + "tool_state": "{\"datasets\": [{\"__index__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"rarefied_table\"}}, {\"__index__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"faith_pd_vector\"}}, {\"__index__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"observed_features_vector\"}}, {\"__index__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"shannon_vector\"}}, {\"__index__\": 4, \"input\": {\"__class__\": \"ConnectedValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"eveness_vector\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.2.0", + "type": "tool", + "uuid": "032f5d65-2ed6-47b2-8837-25aa360fd355", + "when": null, + "workflow_outputs": [ + { + "label": "Richness and evenness collection", + "output_name": "output", + "uuid": "b17fd336-7d7c-4b1f-a0ef-0337323ba9d5" + } + ] + } + }, + "tags": [], + "uuid": "300b5a7d-f763-486a-a8ea-87ea84571f19", + "version": 2 +} diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/README.md b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/README.md new file mode 100644 index 000000000..55a291454 --- /dev/null +++ b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/README.md @@ -0,0 +1,70 @@ +# QIIME2 workflows + +## Available workflows + +- III-V Downstream analyses: III) reconstruct a taxonomy for diversity analysis, IV) rarefaction analysis, V) taxonomic analysis. +- VI: Computation of diversity metrics and estimations + +Analogous to the procedures described in the Parkinson’s Mouse Tutorial: https://docs.qiime2.org/2024.5/tutorials/pd-mice/ + +## Inputs + +The two workflows have two inputs in common + +- Feature table: Count data +- Metadata: Metadata table + +and the following extra inputs + +III-V + +- Representative sequences: Representative (ASV) sequences +- Minimum depth: Lower limit of the sampling depth for the alpha rarefaction analysis +- Maximum depth: Upper limit of the sampling depth for the alpha rarefaction analysis +- SEPP fragment insertion reference: used for the reconstruction of the phylogenetic tree +- Taxonomic classifier: The classifier to assign taxonomic information to the ASVs + +VI: + +Sampling depth: For the metric calculation (should be based on the rarefaction analysis done in IV) +Target metadata parameter: that should be used for beta diversity calculations +Rooted Tree: for instance the tree computed in III + +## Processing + +III-V + +- Phylogenetic tree generation using `qiime2 fragment-insertion sepp` +- Alpha rarefaction analysis using `qiime2 diversity alpha-rarefaction` +- Taxonomic classification using `qiime2 feature-classifier classify-sklearn` and compute barplot and tabular output + +VI: + +- compute alpha and beta diversity metrics using `qiime2 diversity core-metrics-phylogenetic` +- organize these metrics in 4 collections: + 1. Distance matrix collection (weighted and unweighted unifrac, jaccard and bray curtis) + 2. PCoA collection (same as the distance matrices) + 3. Emperor plot collection (same as the distance matrices) + 4. Richness and evenness collection (rarefied table, faith pd vector observed features vector, shannon vector, evenness vector) +- get visualization for alpha diversity: + - Pielou's eveness + - Observed features + - Shannons diversity index +- get visualization for beta diversity + - Jaccard distance matrix + - Bray curtis distance matrix + - Unifrac distance metrix + +## Outputs + +III-V: + +- Phylogenetic tree +- Rarefaction curve +- Taxonomic classification (as qza, barplot and table) + +VI: + +- Four collections containing: distance matrix, PCoA, Emperor plots, Richness and evenness +- Visualization for alpha diversity: Pielou's eveness, Observed features, Shannons diversity index +- Visualization for beta diversity: Jaccard, Bray curtis, Unifrac \ No newline at end of file diff --git a/workflows/bacterial_genomics/amr_gene_detection/CHANGELOG.md b/workflows/bacterial_genomics/amr_gene_detection/CHANGELOG.md index 2e02859a8..bbeba9871 100644 --- a/workflows/bacterial_genomics/amr_gene_detection/CHANGELOG.md +++ b/workflows/bacterial_genomics/amr_gene_detection/CHANGELOG.md @@ -1,5 +1,17 @@ # Changelog +## [1.1.3] 2024-09-30 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0` + +## [1.1.2] 2024-09-19 + +### Manual update + +- Change percent identity threshold for Resfinder blast results in StarAMR from 98.0% to 90.0% + ## [1.1.1] 2024-07-08 ### Automatic update diff --git a/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection-tests.yml b/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection-tests.yml index c7a1de448..a3ef9036f 100644 --- a/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection-tests.yml +++ b/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection-tests.yml @@ -5,58 +5,58 @@ path: https://zenodo.org/records/11488310/files/shovill_contigs_fasta outputs: staramr_detailed_summary: - assert: - has_text: - text: "Resistance" - has_n_columns: - n: 12 + asserts: + has_text: + text: "Resistance" + has_n_columns: + n: 12 staramr_resfinder_report: - assert: - has_text: - text: "tetracycline" - has_n_columns: - n: 13 + asserts: + has_text: + text: "tetracycline" + has_n_columns: + n: 13 staramr_mlst_report: - assert: + asserts: has_text: text: "efaecalis" has_n_columns: n: 10 staramr_plasmidfinder_report: - assert: + asserts: has_text: text: "CP002494" has_n_columns: n: 9 staramr_summary: - assert: + asserts: has_text: text: "streptomycin" has_n_columns: n: 12 amrfinderplus_report: - assert: + asserts: has_text: text: "Enterococcus faecalis quinolone resistant ParC" has_n_columns: n: 23 amrfinderplus_mutation: - assert: + asserts: has_text: text: "cardiolipin synthase Cls" has_n_columns: n: 23 abricate_virulence_report: - assert: + asserts: has_text: text: "endocarditis specific antigen" has_n_columns: n: 15 tooldistillator_summarize: - assert: - has_text: + asserts: + - that: "has_text" text: "% Identity to reference sequence" - has_text: + - that: "has_text" text: "Enterococcus faecalis V583" - has_text: - text: "CGE Predicted Phenotype" + - that: "has_text" + text: "Fibrinogen binding protein" diff --git a/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection.ga b/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection.ga index 16290adad..9f83b43bc 100644 --- a/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection.ga +++ b/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection.ga @@ -27,7 +27,7 @@ ], "format-version": "0.1", "license": "GPL-3.0-or-later", - "release": "1.1.1", + "release": "1.1.3", "name": "amr_gene_detection", "steps": { "0": { @@ -311,7 +311,7 @@ "owner": "nml", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"advanced\": {\"pid_threshold\": \"98.0\", \"plength_resfinder\": \"60.0\", \"plength_pointfinder\": \"95.0\", \"plength_plasmidfinder\": \"60.0\", \"genome_size_lower_bound\": \"4000000\", \"genome_size_upper_bound\": \"6000000\", \"minimum_N50_value\": \"10000\", \"minimum_contig_length\": \"300\", \"unacceptable_number_contigs\": \"1000\", \"report_all_blast\": false, \"exclude_negatives\": false, \"exclude_resistance_phenotypes\": false, \"mlst_scheme\": \"auto\", \"exclude_genes\": {\"exclude_genes_condition\": \"default\", \"__current_case__\": 0}, \"complex_mutations\": {\"complex_mutations_condition\": \"default\", \"__current_case__\": 0}, \"plasmidfinder_type\": \"include_all\"}, \"genomes\": {\"__class__\": \"ConnectedValue\"}, \"pointfinder_db\": {\"use_pointfinder\": \"disabled\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"advanced\": {\"pid_threshold\": \"90.0\", \"plength_resfinder\": \"60.0\", \"plength_pointfinder\": \"95.0\", \"plength_plasmidfinder\": \"60.0\", \"genome_size_lower_bound\": \"4000000\", \"genome_size_upper_bound\": \"6000000\", \"minimum_N50_value\": \"10000\", \"minimum_contig_length\": \"300\", \"unacceptable_number_contigs\": \"1000\", \"report_all_blast\": false, \"exclude_negatives\": false, \"exclude_resistance_phenotypes\": false, \"mlst_scheme\": \"auto\", \"exclude_genes\": {\"exclude_genes_condition\": \"default\", \"__current_case__\": 0}, \"complex_mutations\": {\"complex_mutations_condition\": \"default\", \"__current_case__\": 0}, \"plasmidfinder_type\": \"include_all\"}, \"genomes\": {\"__class__\": \"ConnectedValue\"}, \"pointfinder_db\": {\"use_pointfinder\": \"disabled\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.10.0+galaxy1", "type": "tool", "uuid": "10eed503-9e5b-4acf-8cd8-29e81d7668a5", @@ -528,7 +528,7 @@ }, "7": { "annotation": "ToolDistillator extracts results from tools and creates a JSON file for each tool", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0", "errors": null, "id": 7, "input_connections": { @@ -598,15 +598,15 @@ "output_name": "output_json" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "a7387ce2a8ca", + "changeset_revision": "8d6686664021", "name": "tooldistillator", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"log\": false, \"tool_section\": {\"tools\": [{\"__index__\": 0, \"select_tool\": {\"tool_list\": \"abricate\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"1.0.1\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"select_tool\": {\"tool_list\": \"staramr\", \"__current_case__\": 20, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mlst_file_path\": {\"__class__\": \"ConnectedValue\"}, \"plasmidfinder_file_path\": {\"__class__\": \"RuntimeValue\"}, \"pointfinder_file_path\": {\"__class__\": \"RuntimeValue\"}, \"setting_file_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"0.10.0\", \"reference_database_version\": null}}, {\"__index__\": 2, \"select_tool\": {\"tool_list\": \"amrfinderplus\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}, \"point_mutation_report_path\": {\"__class__\": \"ConnectedValue\"}, \"nucleotide_sequence_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"3.12.8\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.9+galaxy0", + "tool_version": "0.9.1+galaxy0", "type": "tool", "uuid": "1589f8a1-65b6-43f0-9e75-cad9b1752e5c", "when": null, @@ -620,7 +620,7 @@ }, "8": { "annotation": "ToolDistillator summarize groups all JSON file into a unique JSON file", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0", "errors": null, "id": 8, "input_connections": { @@ -658,15 +658,15 @@ "output_name": "summary_json" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "def7a82d23e1", + "changeset_revision": "f3233d395549", "name": "tooldistillator_summarize", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"summarize_data\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.9+galaxy0", + "tool_version": "0.9.1+galaxy0", "type": "tool", "uuid": "a88f6b82-502c-46cf-a174-2c8361e8e8dd", "when": null, diff --git a/workflows/bacterial_genomics/bacterial_genome_annotation/CHANGELOG.md b/workflows/bacterial_genomics/bacterial_genome_annotation/CHANGELOG.md index b7ca5db4a..a484bdfad 100644 --- a/workflows/bacterial_genomics/bacterial_genome_annotation/CHANGELOG.md +++ b/workflows/bacterial_genomics/bacterial_genome_annotation/CHANGELOG.md @@ -1,5 +1,22 @@ # Changelog +## [1.1.5] 2024-09-30 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0` + +## [1.1.4] 2024-09-19 + +### Manual update + +- Updated the tool versions manually in the ToolDistillator parameters + +## [1.1.3] 2024-09-09 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.4+galaxy0` + ## [1.1.2] - 2024-07-19 - PlasmidFinder database correction in .ga diff --git a/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation-tests.yml b/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation-tests.yml index 96a7fc4de..96b577b03 100644 --- a/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation-tests.yml +++ b/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation-tests.yml @@ -8,54 +8,52 @@ Select a AMRFinderPlus database: amrfinderplus_V3.12_2024-05-02.2 outputs: integronfinder2_logfile_text: - assert: + asserts: has_text: text: "Writing out results for replicon" integronfinder2_summary: - assert: - has_n_columns: - n: 6 + asserts: + has_text: + text: "contig00001" integronfinder2_results_tabular: - assert: - has_n_columns: - n: 14 + asserts: + has_text: + text: "contig00009_42" bakta_hypothetical_tabular: - assert: - has_n_columns: - n: 9 + asserts: + has_text: + text: "DHJLLP_04750" bakta_annotation_json: - assert: + asserts: has_text: text: "aa_hexdigest" bakta_annotation_tabular: - assert: - has_n_columns: - n: 9 + asserts: + has_text: + text: "Phosphotransferase system cellobiose-specific component IIC" isescan_results_tabular: - assert: - has_n_columns: - n: 24 + asserts: + has_text: + text: "IS256_162" isescan_summary_tabular: - assert: + asserts: has_text: text: "nIS" isescan_logfile_text: - assert: + asserts: has_text: text: "Both complete and partial IS elements are reported." plasmidfinder_result_json: - assert: + asserts: has_text: text: "positions_in_contig" plasmidfinder_results_tabular: - assert: + asserts: has_n_columns: n: 8 tooldistillator_summarize: - assert: - has_text: + asserts: + - that: "has_text" text: "CDS12738(DOp1)" - has_text: - text: "CALIN" - has_text: - text: "insertion_sequence" + - that: "has_text" + text: "PFAM" \ No newline at end of file diff --git a/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation.ga b/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation.ga index ccb7df177..17b5af4c6 100644 --- a/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation.ga +++ b/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation.ga @@ -27,7 +27,7 @@ ], "format-version": "0.1", "license": "GPL-3.0-or-later", - "release": "1.1.2", + "release": "1.1.5", "name": "bacterial_genome_annotation", "steps": { "0": { @@ -632,7 +632,7 @@ }, "7": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.4+galaxy0", "errors": null, "id": 7, "input_connections": { @@ -905,15 +905,15 @@ "output_name": "summary_txt" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.4+galaxy0", "tool_shed_repository": { - "changeset_revision": "ba6990f72184", + "changeset_revision": "d77802fe76f7", "name": "bakta", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"annotation\": {\"complete\": false, \"prodigal\": {\"__class__\": \"RuntimeValue\"}, \"translation_table\": \"11\", \"keep_contig_headers\": false, \"replicons\": {\"__class__\": \"RuntimeValue\"}, \"compliant\": false, \"proteins\": {\"__class__\": \"RuntimeValue\"}, \"meta\": false, \"regions\": {\"__class__\": \"RuntimeValue\"}}, \"input_option\": {\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"min_contig_length\": null, \"bakta_db_select\": {\"__class__\": \"ConnectedValue\"}, \"amrfinder_db_select\": {\"__class__\": \"ConnectedValue\"}}, \"organism\": {\"genus\": null, \"species\": null, \"strain\": null, \"plasmid\": null}, \"output_files\": {\"output_selection\": [\"file_tsv\", \"file_gff3\", \"file_ffn\", \"file_plot\", \"file_gbff\", \"file_embl\", \"file_fna\", \"file_faa\", \"hypo_tsv\", \"hypo_fa\", \"file_json\", \"sum_txt\"]}, \"workflow\": {\"skip_analysis\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.9.3+galaxy0", + "tool_version": "1.9.4+galaxy0", "type": "tool", "uuid": "0a32dcad-f456-460e-9e6f-9e306a8fd515", "when": null, @@ -982,7 +982,7 @@ }, "8": { "annotation": "ToolDistillator extracts results from tools and creates a JSON file for each tool", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0", "errors": null, "id": 8, "input_connections": { @@ -1120,15 +1120,15 @@ "output_name": "output_json" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "a7387ce2a8ca", + "changeset_revision": "8d6686664021", "name": "tooldistillator", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"log\": false, \"tool_section\": {\"tools\": [{\"__index__\": 0, \"select_tool\": {\"tool_list\": \"plasmidfinder\", \"__current_case__\": 14, \"input\": {\"__class__\": \"ConnectedValue\"}, \"plasmid_result_tabular_path\": {\"__class__\": \"ConnectedValue\"}, \"genome_hit_path\": {\"__class__\": \"ConnectedValue\"}, \"plasmid_hit_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"2.1.6\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"select_tool\": {\"tool_list\": \"isescan\", \"__current_case__\": 11, \"input\": {\"__class__\": \"ConnectedValue\"}, \"summary_path\": {\"__class__\": \"ConnectedValue\"}, \"annotation_path\": {\"__class__\": \"ConnectedValue\"}, \"orf_fna_path\": {\"__class__\": \"ConnectedValue\"}, \"orf_faa_path\": {\"__class__\": \"ConnectedValue\"}, \"is_fna_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"1.7.2.3\", \"reference_database_version\": null}}, {\"__index__\": 2, \"select_tool\": {\"tool_list\": \"integronfinder2\", \"__current_case__\": 10, \"input\": {\"__class__\": \"ConnectedValue\"}, \"summary_file_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"2.0.2\", \"reference_database_version\": null}}, {\"__index__\": 3, \"select_tool\": {\"tool_list\": \"bakta\", \"__current_case__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}, \"annotation_tabular_path\": {\"__class__\": \"ConnectedValue\"}, \"annotation_genbank_path\": {\"__class__\": \"ConnectedValue\"}, \"annotation_embl_path\": {\"__class__\": \"ConnectedValue\"}, \"contig_sequences_path\": {\"__class__\": \"ConnectedValue\"}, \"hypothetical_protein_path\": {\"__class__\": \"ConnectedValue\"}, \"hypothetical_tabular_path\": {\"__class__\": \"ConnectedValue\"}, \"plot_file_path\": {\"__class__\": \"ConnectedValue\"}, \"summary_result_path\": {\"__class__\": \"ConnectedValue\"}, \"nucleotide_annotation_path\": {\"__class__\": \"ConnectedValue\"}, \"amino_acid_annotation_path\": {\"__class__\": \"ConnectedValue\"}, \"gff_file_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"1.9.3\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.9+galaxy0", + "tool_state": "{\"log\": false, \"tool_section\": {\"tools\": [{\"__index__\": 0, \"select_tool\": {\"tool_list\": \"plasmidfinder\", \"__current_case__\": 14, \"input\": {\"__class__\": \"ConnectedValue\"}, \"plasmid_result_tabular_path\": {\"__class__\": \"ConnectedValue\"}, \"genome_hit_path\": {\"__class__\": \"ConnectedValue\"}, \"plasmid_hit_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"2.1.6\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"select_tool\": {\"tool_list\": \"isescan\", \"__current_case__\": 11, \"input\": {\"__class__\": \"ConnectedValue\"}, \"summary_path\": {\"__class__\": \"ConnectedValue\"}, \"annotation_path\": {\"__class__\": \"ConnectedValue\"}, \"orf_fna_path\": {\"__class__\": \"ConnectedValue\"}, \"orf_faa_path\": {\"__class__\": \"ConnectedValue\"}, \"is_fna_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"1.7.2.3\", \"reference_database_version\": null}}, {\"__index__\": 2, \"select_tool\": {\"tool_list\": \"integronfinder2\", \"__current_case__\": 10, \"input\": {\"__class__\": \"ConnectedValue\"}, \"summary_file_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"2.0.5\", \"reference_database_version\": null}}, {\"__index__\": 3, \"select_tool\": {\"tool_list\": \"bakta\", \"__current_case__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}, \"annotation_tabular_path\": {\"__class__\": \"ConnectedValue\"}, \"annotation_genbank_path\": {\"__class__\": \"ConnectedValue\"}, \"annotation_embl_path\": {\"__class__\": \"ConnectedValue\"}, \"contig_sequences_path\": {\"__class__\": \"ConnectedValue\"}, \"hypothetical_protein_path\": {\"__class__\": \"ConnectedValue\"}, \"hypothetical_tabular_path\": {\"__class__\": \"ConnectedValue\"}, \"plot_file_path\": {\"__class__\": \"ConnectedValue\"}, \"summary_result_path\": {\"__class__\": \"ConnectedValue\"}, \"nucleotide_annotation_path\": {\"__class__\": \"ConnectedValue\"}, \"amino_acid_annotation_path\": {\"__class__\": \"ConnectedValue\"}, \"gff_file_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"1.9.4\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.9.1+galaxy0", "type": "tool", "uuid": "678bdbfe-7a3a-4a91-8ea7-1cb17f53daa6", "when": null, @@ -1142,7 +1142,7 @@ }, "9": { "annotation": "ToolDistillator summarize groups all JSON file into a unique JSON file", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0", "errors": null, "id": 9, "input_connections": { @@ -1180,15 +1180,15 @@ "output_name": "summary_json" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "def7a82d23e1", + "changeset_revision": "f3233d395549", "name": "tooldistillator_summarize", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"summarize_data\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.9+galaxy0", + "tool_version": "0.9.1+galaxy0", "type": "tool", "uuid": "3427b1f1-79ce-4ade-a350-baf15ac250c2", "when": null, @@ -1211,4 +1211,4 @@ ], "uuid": "d55a9e46-a205-4143-b92f-3783499063ed", "version": 1 -} +} \ No newline at end of file diff --git a/workflows/computational-chemistry/fragment-based-docking-scoring/fragment-based-docking-scoring-tests.yml b/workflows/computational-chemistry/fragment-based-docking-scoring/fragment-based-docking-scoring-tests.yml index c514aa209..5da14f26d 100644 --- a/workflows/computational-chemistry/fragment-based-docking-scoring/fragment-based-docking-scoring-tests.yml +++ b/workflows/computational-chemistry/fragment-based-docking-scoring/fragment-based-docking-scoring-tests.yml @@ -21,10 +21,11 @@ SuCOS threshold: 0 outputs: Scored and filtered poses: - class: File - assert: - has_line: "$$$$" - n: 4 - assert: - has_test: "SuCOS_Score" - n: 4 + asserts: + has_line: + line: "$$$$" + n: 4 + asserts: + has_text: + text: "SuCOS_Score" + n: 4 diff --git a/workflows/epigenetics/atacseq/CHANGELOG.md b/workflows/epigenetics/atacseq/CHANGELOG.md index 45148b198..4b0e6dc95 100644 --- a/workflows/epigenetics/atacseq/CHANGELOG.md +++ b/workflows/epigenetics/atacseq/CHANGELOG.md @@ -1,5 +1,16 @@ # Changelog +## [0.17] 2024-09-23 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1` +- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0` + +### Manual update +- Add a step to remove comments lines from histogram to be compatible with new multiQC version + ## [0.16] 2024-07-15 ### Automatic update diff --git a/workflows/epigenetics/atacseq/atacseq-tests.yml b/workflows/epigenetics/atacseq/atacseq-tests.yml index 133f508b1..1b2a1961d 100644 --- a/workflows/epigenetics/atacseq/atacseq-tests.yml +++ b/workflows/epigenetics/atacseq/atacseq-tests.yml @@ -98,31 +98,11 @@ value: 1133795 delta: 100000 'MultiQC on input dataset(s): Stats': - element_tests: - bowtie2: - asserts: - has_line: - line: "SRR891268_chr22_enriched\t280964\t280964\t30410\t109333\t141221\t13319\t6127\t6515\t21540\t98.91\t10770.0\t3063.5\t3257.5" - cutadapt: - asserts: - has_line: - line: "SRR891268_chr22_enriched_2\t4.9\t285247\t41011\t40415\t4283\t280964\t28524700\t480633\t27163516\t4.771948521807416" - general_stats: - asserts: - has_text: - text: "SRR891268_chr22_enriched\t200.0\t223\t0.028469\t98.91" - macs: - asserts: - has_line: - line: "SRR891268_chr22_enriched\t223\t47.0\t232804.0\t200.0" - picard_dups: - asserts: - has_line: - line: "SRR891268_chr22_enriched\tUnknown Library\t0.0\t119813.0\t0.0\t0.0\t0.0\t3411.0\t5.0\t0.028469\t2067029.0" - sources: - asserts: - has_n_lines: - n: 4 + asserts: + has_line: + line: "Sample MACS2_mqc_generalstats_macs2_d MACS2_mqc_generalstats_macs2_peak_count Picard: Mark Duplicates_mqc_generalstats_picard_mark_duplicates_PERCENT_DUPLICATION Bowtie 2 / HiSAT2_mqc_generalstats_bowtie_2_hisat2_overall_alignment_rate Cutadapt_mqc_generalstats_cutadapt_percent_trimmed" + has_text_matching: + expression: "SRR891268_chr22_enriched\t200.0\t223\t2.8[0-9]*\t98.[0-9]*\t4.7[0-9]*" MultiQC webpage: asserts: - that: "has_text" diff --git a/workflows/epigenetics/atacseq/atacseq.ga b/workflows/epigenetics/atacseq/atacseq.ga index 6d7327a26..a885049d5 100644 --- a/workflows/epigenetics/atacseq/atacseq.ga +++ b/workflows/epigenetics/atacseq/atacseq.ga @@ -1,6 +1,7 @@ { "a_galaxy_workflow": "true", "annotation": "This workflow takes as input a collection of paired fastq. It will remove bad quality and adapters with cutadapt. Map with Bowtie2 end-to-end. Will remove reads on MT and unconcordant pairs and pairs with mapping quality below 30 and PCR duplicates. Will compute the pile-up on 5' +- 100bp. Will call peaks and count the number of reads falling in the 1kb region centered on the summit. Will compute 2 normalization for coverage: normalized by million reads and normalized by million reads in peaks. Will plot the number of reads for each fragment length.", + "comments": [], "creator": [ { "class": "Person", @@ -10,7 +11,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.16", + "release": "0.17", "name": "ATACseq", "steps": { "0": { @@ -123,7 +124,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "errors": null, "id": 4, "input_connections": { @@ -173,15 +174,15 @@ "output_name": "report" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "aa784cb3810d", + "changeset_revision": "5eb7e84243f2", "name": "cutadapt", "owner": "lparsons", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"adapter_options\": {\"action\": \"trim\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"minimum_length2\": null, \"maximum_length\": null, \"maximum_length2\": null, \"max_n\": null, \"max_expected_errors\": null, \"max_average_error_rate\": null, \"discard_casava\": false, \"pair_filter\": \"any\"}, \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Nextera R1\", \"adapter\": \"CTGTCTCTTATACACATCTCCGAGCCCACGAGAC\"}, \"single_noindels\": false}], \"front_adapters\": [], \"anywhere_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Nextera R2\", \"adapter\": \"CTGTCTCTTATACACATCTGACGCTGCCGACGA\"}, \"single_noindels\": false}], \"front_adapters2\": [], \"anywhere_adapters2\": []}, \"pair_adapters\": false}, \"other_trimming_options\": {\"cut\": \"0\", \"cut2\": \"0\", \"quality_cutoff\": \"30\", \"quality_cutoff2\": \"\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"poly_a\": false, \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"shorten_options_r2\": {\"shorten_values_r2\": \"False\", \"__current_case__\": 1}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"strip_suffix\": \"\", \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.9+galaxy0", + "tool_version": "4.9+galaxy1", "type": "tool", "uuid": "33fa2759-9f3f-431b-b35c-b5c777d5d5b7", "when": null, @@ -477,7 +478,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -605,7 +606,7 @@ }, "12": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "errors": null, "id": 12, "input_connections": { @@ -634,15 +635,15 @@ "output_name": "outputcnt" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "tool_shed_repository": { - "changeset_revision": "6be888be75f9", + "changeset_revision": "32dc5f781059", "name": "samtools_view", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"all_reads\", \"__current_case__\": 0, \"output_options\": {\"reads_report_type\": \"count\", \"__current_case__\": 1}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.15.1+galaxy2", + "tool_version": "1.20+galaxy3", "type": "tool", "uuid": "2999f836-c74f-47ed-b1ad-81f43349fe11", "when": null, @@ -789,9 +790,53 @@ }, "14": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1", "errors": null, "id": 14, + "input_connections": { + "infile": { + "id": 11, + "output_name": "output2" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Search in textfiles", + "name": "infile" + } + ], + "label": "remove comments lines", + "name": "Search in textfiles", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 1780, + "top": 701.4833374023438 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "86755160afbf", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"case_sensitive\": \"-i\", \"color\": \"NOCOLOR\", \"infile\": {\"__class__\": \"RuntimeValue\"}, \"invert\": \"-v\", \"lines_after\": \"0\", \"lines_before\": \"0\", \"regex_type\": \"-P\", \"url_paste\": \"^#\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "9.3+galaxy1", + "type": "tool", + "uuid": "c06960f8-9d4e-483e-8f07-12976f8b802a", + "when": null, + "workflow_outputs": [] + }, + "15": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", + "errors": null, + "id": 15, "input_connections": { "input": { "id": 12, @@ -818,25 +863,25 @@ "output_name": "out_file1" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", "tool_shed_repository": { - "changeset_revision": "6595517c2dd8", + "changeset_revision": "aff5135563c6", "name": "column_maker", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"avoid_scientific_notation\": true, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"1000000/c1\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"1\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.0", + "tool_version": "2.1", "type": "tool", "uuid": "ec62cddf-fb04-4185-b9f4-709de2ce0202", "when": null, "workflow_outputs": [] }, - "15": { + "16": { "annotation": "", "content_id": "wig_to_bigWig", "errors": null, - "id": 15, + "id": 16, "input_connections": { "input1": { "id": 13, @@ -879,11 +924,11 @@ } ] }, - "16": { + "17": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.31.1+galaxy0", "errors": null, - "id": 16, + "id": 17, "input_connections": { "genome_file_opts|genome": { "id": 1, @@ -940,11 +985,11 @@ "when": null, "workflow_outputs": [] }, - "17": { + "18": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1", "errors": null, - "id": 17, + "id": 18, "input_connections": { "infile": { "id": 13, @@ -982,7 +1027,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1000,14 +1045,14 @@ } ] }, - "18": { + "19": { "annotation": "", "content_id": "param_value_from_file", "errors": null, - "id": 18, + "id": 19, "input_connections": { "input1": { - "id": 14, + "id": 15, "output_name": "out_file1" } }, @@ -1039,14 +1084,14 @@ "when": null, "workflow_outputs": [] }, - "19": { + "20": { "annotation": "", "content_id": "__APPLY_RULES__", "errors": null, - "id": 19, + "id": 20, "input_connections": { "input": { - "id": 15, + "id": 16, "output_name": "out_file1" } }, @@ -1078,14 +1123,14 @@ "when": null, "workflow_outputs": [] }, - "20": { + "21": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1", "errors": null, - "id": 20, + "id": 21, "input_connections": { "input": { - "id": 16, + "id": 17, "output_name": "output" } }, @@ -1131,22 +1176,22 @@ } ] }, - "21": { + "22": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.4+galaxy0", "errors": null, - "id": 21, + "id": 22, "input_connections": { "advancedOpt|binSize": { "id": 3, "output_name": "output" }, "advancedOpt|scaleFactors": { - "id": 18, + "id": 19, "output_name": "text_param" }, "bigwigs": { - "id": 19, + "id": 20, "output_name": "output" } }, @@ -1205,14 +1250,14 @@ } ] }, - "22": { + "23": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.31.1+galaxy0", "errors": null, - "id": 22, + "id": 23, "input_connections": { "inputA": { - "id": 20, + "id": 21, "output_name": "output" }, "reduce_or_iterate|inputB": { @@ -1266,14 +1311,14 @@ "when": null, "workflow_outputs": [] }, - "23": { + "24": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "errors": null, - "id": 23, + "id": 24, "input_connections": { "infile": { - "id": 22, + "id": 23, "output_name": "output" } }, @@ -1308,7 +1353,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1326,14 +1371,14 @@ } ] }, - "24": { + "25": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", "errors": null, - "id": 24, + "id": 25, "input_connections": { "input": { - "id": 23, + "id": 24, "output_name": "outfile" } }, @@ -1357,28 +1402,28 @@ "output_name": "out_file1" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", "tool_shed_repository": { - "changeset_revision": "6595517c2dd8", + "changeset_revision": "aff5135563c6", "name": "column_maker", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"avoid_scientific_notation\": true, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"1000000/c1\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"1\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.0", + "tool_version": "2.1", "type": "tool", "uuid": "5f55e258-a4fe-4b51-ab9b-2a6f0f22d910", "when": null, "workflow_outputs": [] }, - "25": { + "26": { "annotation": "", "content_id": "cat1", "errors": null, - "id": 25, + "id": 26, "input_connections": { "input1": { - "id": 23, + "id": 24, "output_name": "outfile" }, "queries_0|input2": { @@ -1414,14 +1459,14 @@ "when": null, "workflow_outputs": [] }, - "26": { + "27": { "annotation": "", "content_id": "param_value_from_file", "errors": null, - "id": 26, + "id": 27, "input_connections": { "input1": { - "id": 24, + "id": 25, "output_name": "out_file1" } }, @@ -1453,14 +1498,14 @@ "when": null, "workflow_outputs": [] }, - "27": { + "28": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "errors": null, - "id": 27, + "id": 28, "input_connections": { "infile": { - "id": 25, + "id": 26, "output_name": "out_file1" } }, @@ -1486,7 +1531,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1498,22 +1543,22 @@ "when": null, "workflow_outputs": [] }, - "28": { + "29": { "annotation": "Isolate each bigwig do normalize not average", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.4+galaxy0", "errors": null, - "id": 28, + "id": 29, "input_connections": { "advancedOpt|binSize": { "id": 3, "output_name": "output" }, "advancedOpt|scaleFactors": { - "id": 26, + "id": 27, "output_name": "text_param" }, "bigwigs": { - "id": 19, + "id": 20, "output_name": "output" } }, @@ -1572,11 +1617,11 @@ } ] }, - "29": { + "30": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "errors": null, - "id": 29, + "id": 30, "input_connections": { "results_0|software_cond|input": { "id": 4, @@ -1595,15 +1640,15 @@ "output_name": "metrics_file" }, "results_4|software_cond|input": { - "id": 11, - "output_name": "output2" + "id": 14, + "output_name": "output" }, "results_5|software_cond|input": { "id": 13, "output_name": "output_tabular" }, "results_6|software_cond|input": { - "id": 27, + "id": 28, "output_name": "outfile" } }, @@ -1611,10 +1656,6 @@ "label": null, "name": "MultiQC", "outputs": [ - { - "name": "stats", - "type": "input" - }, { "name": "plots", "type": "input" @@ -1622,6 +1663,10 @@ { "name": "html_report", "type": "html" + }, + { + "name": "stats", + "type": "tabular" } ], "position": { @@ -1635,15 +1680,15 @@ "output_name": "plots" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "abfd8a6544d7", + "changeset_revision": "f7e2f1eb3a16", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"bowtie2\", \"__current_case__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 32, \"plot_type\": \"bargraph\", \"section_name\": \"chrM\", \"title\": \"reads mapping on chrM\", \"description\": \"\", \"xlab\": \"\", \"ylab\": \"\", \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 3, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}, {\"__index__\": 4, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 32, \"plot_type\": \"linegraph\", \"section_name\": \"Fragment size\", \"title\": \"Fragment size distribution\", \"description\": \"\", \"xlab\": \"\", \"ylab\": \"\", \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 5, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 6, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 32, \"plot_type\": \"bargraph\", \"section_name\": \"Reads in peaks\", \"title\": \"Number of reads in peaks\", \"description\": \"Number of reads falling 500bp from a summit\", \"xlab\": \"\", \"ylab\": \"\", \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.11+galaxy1", + "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"bowtie2\", \"__current_case__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 32, \"plot_type\": \"bargraph\", \"section_name\": \"chrM\", \"title\": \"reads mapping on chrM\", \"description\": \"\", \"xlab\": \"\", \"ylab\": \"\", \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 3, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}, {\"__index__\": 4, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 32, \"plot_type\": \"linegraph\", \"section_name\": \"Fragment size\", \"title\": \"Fragment size distribution\", \"description\": \"\", \"xlab\": \"\", \"ylab\": \"\", \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 5, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 6, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 32, \"plot_type\": \"bargraph\", \"section_name\": \"Reads in peaks\", \"title\": \"Number of reads in peaks\", \"description\": \"Number of reads falling 500bp from a summit\", \"xlab\": \"\", \"ylab\": \"\", \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "112d720f-c747-4c92-985f-ebdb52086cc9", "when": null, @@ -1664,6 +1709,6 @@ "tags": [ "ATACseq" ], - "uuid": "02785f0c-c445-4419-9f95-a202eaf6493a", + "uuid": "9debc3c9-ccbd-4ce6-a7de-80580e663cac", "version": 1 } \ No newline at end of file diff --git a/workflows/epigenetics/average-bigwig-between-replicates/average-bigwig-between-replicates-tests.yml b/workflows/epigenetics/average-bigwig-between-replicates/average-bigwig-between-replicates-tests.yml index 3f21209d2..7484600c3 100644 --- a/workflows/epigenetics/average-bigwig-between-replicates/average-bigwig-between-replicates-tests.yml +++ b/workflows/epigenetics/average-bigwig-between-replicates/average-bigwig-between-replicates-tests.yml @@ -23,8 +23,8 @@ bin_size: 50 outputs: average_bigwigs: - class: Collection - collection_type: list + attributes: + collection_type: list element_tests: ATAC_HH19_PT: asserts: diff --git a/workflows/epigenetics/chipseq-pe/CHANGELOG.md b/workflows/epigenetics/chipseq-pe/CHANGELOG.md index 902e9525a..b2ca81d15 100644 --- a/workflows/epigenetics/chipseq-pe/CHANGELOG.md +++ b/workflows/epigenetics/chipseq-pe/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.12] 2024-09-23 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0` + ## [0.11] 2024-07-15 ### Automatic update diff --git a/workflows/epigenetics/chipseq-pe/chipseq-pe-tests.yml b/workflows/epigenetics/chipseq-pe/chipseq-pe-tests.yml index 7817a8d66..30f746b1b 100644 --- a/workflows/epigenetics/chipseq-pe/chipseq-pe-tests.yml +++ b/workflows/epigenetics/chipseq-pe/chipseq-pe-tests.yml @@ -31,27 +31,11 @@ - that: "has_text" text: Bowtie 2 / HiSAT2 'MultiQC on input dataset(s): Stats': - element_tests: - bowtie2: - asserts: - has_text: - text: "46307\t46307\t1292" - cutadapt: - asserts: - has_text: - text: "4.9\t50000\t587\t550\t3693\t46307\t5100000" - general_stats: - asserts: - has_text: - text: "201.0\t0.0\t11\t98.68" - macs: - asserts: - has_text: - text: "11\t201.0\t41724.0\t41724.0\t1.0" - sources: - asserts: - has_n_lines: - n: 3 + asserts: + has_line: + line: "Sample MACS2_mqc_generalstats_macs2_d MACS2_mqc_generalstats_macs2_treatment_redundant_rate MACS2_mqc_generalstats_macs2_peak_count Bowtie 2 / HiSAT2_mqc_generalstats_bowtie_2_hisat2_overall_alignment_rate Cutadapt_mqc_generalstats_cutadapt_percent_trimmed" + has_text_matching: + expression: "wt_H3K4me3\t201.0\t0.0\t11\t98.[0-9]*\t10.[0-9]*" filtered BAM: element_tests: wt_H3K4me3: diff --git a/workflows/epigenetics/chipseq-pe/chipseq-pe.ga b/workflows/epigenetics/chipseq-pe/chipseq-pe.ga index ffeb5ecc6..d2790c119 100644 --- a/workflows/epigenetics/chipseq-pe/chipseq-pe.ga +++ b/workflows/epigenetics/chipseq-pe/chipseq-pe.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.11", + "release": "0.12", "name": "ChIPseq_PE", "steps": { "0": { @@ -177,7 +177,7 @@ }, "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "errors": null, "id": 6, "input_connections": { @@ -235,15 +235,15 @@ "output_name": "report" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "aa784cb3810d", + "changeset_revision": "5eb7e84243f2", "name": "cutadapt", "owner": "lparsons", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"adapter_options\": {\"action\": \"trim\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"minimum_length2\": null, \"maximum_length\": null, \"maximum_length2\": null, \"max_n\": null, \"max_expected_errors\": null, \"max_average_error_rate\": null, \"discard_casava\": false, \"pair_filter\": \"any\"}, \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC \", \"adapter\": {\"__class__\": \"ConnectedValue\"}}, \"single_noindels\": false}], \"front_adapters\": [], \"anywhere_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Please use: For R2: - For Nextera: CTGTCTCTTATACACATCTGACGCTGCCGACGA - For TruSeq: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT\", \"adapter\": {\"__class__\": \"ConnectedValue\"}}, \"single_noindels\": false}], \"front_adapters2\": [], \"anywhere_adapters2\": []}, \"pair_adapters\": false}, \"other_trimming_options\": {\"cut\": \"0\", \"cut2\": \"0\", \"quality_cutoff\": \"30\", \"quality_cutoff2\": \"\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"poly_a\": false, \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"shorten_options_r2\": {\"shorten_values_r2\": \"False\", \"__current_case__\": 1}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"strip_suffix\": \"\", \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.9+galaxy0", + "tool_version": "4.9+galaxy1", "type": "tool", "uuid": "c7846b4c-54fb-458e-982e-c0d8358a9f5d", "when": null, @@ -578,7 +578,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -645,7 +645,7 @@ }, "12": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "errors": null, "id": 12, "input_connections": { @@ -666,10 +666,6 @@ "label": "MultiQC", "name": "MultiQC", "outputs": [ - { - "name": "stats", - "type": "input" - }, { "name": "plots", "type": "input" @@ -677,6 +673,10 @@ { "name": "html_report", "type": "html" + }, + { + "name": "stats", + "type": "tabular" } ], "position": { @@ -690,15 +690,15 @@ "output_name": "plots" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "abfd8a6544d7", + "changeset_revision": "f7e2f1eb3a16", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"bowtie2\", \"__current_case__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.11+galaxy1", + "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"bowtie2\", \"__current_case__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "fb066848-43df-412a-9767-9613bac7d961", "when": null, diff --git a/workflows/epigenetics/chipseq-sr/CHANGELOG.md b/workflows/epigenetics/chipseq-sr/CHANGELOG.md index 8e0ea5d7a..8bbc5bf4e 100644 --- a/workflows/epigenetics/chipseq-sr/CHANGELOG.md +++ b/workflows/epigenetics/chipseq-sr/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.12] 2024-09-23 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0` + ## [0.11] 2024-07-15 ### Automatic update diff --git a/workflows/epigenetics/chipseq-sr/chipseq-sr-tests.yml b/workflows/epigenetics/chipseq-sr/chipseq-sr-tests.yml index bb6ab5373..19c00d991 100644 --- a/workflows/epigenetics/chipseq-sr/chipseq-sr-tests.yml +++ b/workflows/epigenetics/chipseq-sr/chipseq-sr-tests.yml @@ -22,27 +22,11 @@ - that: "has_text" text: Bowtie 2 / HiSAT2 'MultiQC on input dataset(s): Stats': - element_tests: - bowtie2: - asserts: - has_text: - text: "49251\t49251\t805" - cutadapt: - asserts: - has_text: - text: "4.9\t50000\t587\t749\t49251" - general_stats: - asserts: - has_text_matching: - expression: "200.0\t0.0\t4\t98.[0-9]*\t4.612745098039215" - macs: - asserts: - has_text: - text: "4\t49.0\t44078.0\t44038.0\t1.0\t0.0\t200.0" - sources: - asserts: - has_n_lines: - n: 3 + asserts: + has_line: + line: "Sample MACS2_mqc_generalstats_macs2_d MACS2_mqc_generalstats_macs2_treatment_redundant_rate MACS2_mqc_generalstats_macs2_peak_count Bowtie 2 / HiSAT2_mqc_generalstats_bowtie_2_hisat2_overall_alignment_rate Cutadapt_mqc_generalstats_cutadapt_percent_trimmed" + has_text_matching: + expression: "wt_H3K4me3\t200.0\t0.0\t4\t98.[0-9]*\t4.6[0-9]*" filtered BAM: element_tests: wt_H3K4me3: diff --git a/workflows/epigenetics/chipseq-sr/chipseq-sr.ga b/workflows/epigenetics/chipseq-sr/chipseq-sr.ga index 4a8cdf57b..4c3b60c6c 100644 --- a/workflows/epigenetics/chipseq-sr/chipseq-sr.ga +++ b/workflows/epigenetics/chipseq-sr/chipseq-sr.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.11", + "release": "0.12", "name": "ChIPseq_SR", "steps": { "0": { @@ -150,7 +150,7 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "errors": null, "id": 5, "input_connections": { @@ -204,15 +204,15 @@ "output_name": "report" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "aa784cb3810d", + "changeset_revision": "5eb7e84243f2", "name": "cutadapt", "owner": "lparsons", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adapter_options\": {\"action\": \"trim\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"minimum_length2\": null, \"maximum_length\": null, \"maximum_length2\": null, \"max_n\": null, \"max_expected_errors\": null, \"max_average_error_rate\": null, \"discard_casava\": false, \"pair_filter\": \"any\"}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC\", \"adapter\": {\"__class__\": \"ConnectedValue\"}}, \"single_noindels\": false}], \"front_adapters\": [], \"anywhere_adapters\": []}}, \"other_trimming_options\": {\"cut\": \"0\", \"cut2\": \"0\", \"quality_cutoff\": \"30\", \"quality_cutoff2\": \"\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"poly_a\": false, \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"shorten_options_r2\": {\"shorten_values_r2\": \"False\", \"__current_case__\": 1}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"strip_suffix\": \"\", \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.9+galaxy0", + "tool_version": "4.9+galaxy1", "type": "tool", "uuid": "c7846b4c-54fb-458e-982e-c0d8358a9f5d", "when": null, @@ -547,7 +547,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -614,7 +614,7 @@ }, "11": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "errors": null, "id": 11, "input_connections": { @@ -635,10 +635,6 @@ "label": "MultiQC", "name": "MultiQC", "outputs": [ - { - "name": "stats", - "type": "input" - }, { "name": "plots", "type": "input" @@ -646,6 +642,10 @@ { "name": "html_report", "type": "html" + }, + { + "name": "stats", + "type": "tabular" } ], "position": { @@ -659,15 +659,15 @@ "output_name": "plots" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "abfd8a6544d7", + "changeset_revision": "f7e2f1eb3a16", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"bowtie2\", \"__current_case__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.11+galaxy1", + "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"bowtie2\", \"__current_case__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "fb066848-43df-412a-9767-9613bac7d961", "when": null, diff --git a/workflows/epigenetics/consensus-peaks/CHANGELOG.md b/workflows/epigenetics/consensus-peaks/CHANGELOG.md index 11d873533..95a2698f7 100644 --- a/workflows/epigenetics/consensus-peaks/CHANGELOG.md +++ b/workflows/epigenetics/consensus-peaks/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [1.2] 2024-09-24 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0` + ## [1.1] 2024-05-27 ### Automatic update diff --git a/workflows/epigenetics/consensus-peaks/consensus-peaks-atac-cutandrun.ga b/workflows/epigenetics/consensus-peaks/consensus-peaks-atac-cutandrun.ga index aea947871..7afaa8136 100644 --- a/workflows/epigenetics/consensus-peaks/consensus-peaks-atac-cutandrun.ga +++ b/workflows/epigenetics/consensus-peaks/consensus-peaks-atac-cutandrun.ga @@ -81,7 +81,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "1.1", + "release": "1.2", "name": "Get Confident Peaks From ATAC or CUTandRUN replicates", "steps": { "0": { @@ -239,7 +239,7 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "errors": null, "id": 5, "input_connections": { @@ -268,15 +268,15 @@ "output_name": "outputcnt" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "tool_shed_repository": { - "changeset_revision": "6be888be75f9", + "changeset_revision": "32dc5f781059", "name": "samtools_view", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"all_reads\", \"__current_case__\": 0, \"output_options\": {\"reads_report_type\": \"count\", \"__current_case__\": 1}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.15.1+galaxy2", + "tool_version": "1.20+galaxy3", "type": "tool", "uuid": "9cff58b2-123e-42df-b562-3b2a4a553934", "when": null, @@ -886,7 +886,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -989,7 +989,7 @@ }, "20": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "errors": null, "id": 20, "input_connections": { @@ -1022,15 +1022,15 @@ "output_name": "outputsam" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "tool_shed_repository": { - 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"tool_version": "1.15.1+galaxy2", + "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"selected_reads\", \"__current_case__\": 1, \"filter_config\": {\"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cond_rg\": {\"select_rg\": \"no\", \"__current_case__\": 0}, \"cond_expr\": {\"select_expr\": \"no\", \"__current_case__\": 0}, \"quality\": null, \"library\": null, \"cigarcons\": null, \"inclusive_filter\": null, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"tag\": null, \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"target\", \"__current_case__\": 1, \"target\": {\"__class__\": \"ConnectedValue\"}, \"seed\": \"1\"}}, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"complementary_output\": false, \"adv_output\": {\"readtags\": [], \"collapsecigar\": false}, \"output_format\": {\"oformat\": \"bam\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.20+galaxy3", "type": "tool", "uuid": "36713e3f-6110-41f7-8df1-9a9966400fab", "when": null, @@ -1226,7 +1226,7 @@ }, "24": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "errors": null, "id": 24, "input_connections": { @@ -1243,13 +1243,13 @@ "label": "multiQC", "name": "MultiQC", "outputs": [ - { - "name": "stats", - "type": "input" - }, { "name": "html_report", "type": "html" + }, + { + "name": "stats", + "type": "tabular" } ], "position": { @@ -1263,15 +1263,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "abfd8a6544d7", + "changeset_revision": "f7e2f1eb3a16", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.11+galaxy1", + "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "f7d74248-16e3-4020-8156-caae0e7682ef", "when": null, @@ -1403,7 +1403,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" diff --git a/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-pe.ga b/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-pe.ga index 40fa85952..6a069cc8e 100644 --- a/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-pe.ga +++ b/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-pe.ga @@ -81,7 +81,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "1.1", + "release": "1.2", "name": "Get Confident Peaks From ChIP_PE replicates", "steps": { "0": { @@ -194,7 +194,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "errors": null, "id": 4, "input_connections": { @@ -223,15 +223,15 @@ "output_name": "outputcnt" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "tool_shed_repository": { - "changeset_revision": "6be888be75f9", + "changeset_revision": "32dc5f781059", "name": "samtools_view", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"all_reads\", \"__current_case__\": 0, \"output_options\": {\"reads_report_type\": \"count\", \"__current_case__\": 1}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.15.1+galaxy2", + "tool_version": "1.20+galaxy3", "type": "tool", "uuid": "a864ff43-af08-436a-aa78-54491ff0cce6", "when": null, @@ -841,7 +841,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -944,7 +944,7 @@ }, "19": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "errors": null, "id": 19, "input_connections": { @@ -977,15 +977,15 @@ "output_name": "outputsam" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "tool_shed_repository": { - "changeset_revision": "6be888be75f9", + "changeset_revision": "32dc5f781059", "name": "samtools_view", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"selected_reads\", \"__current_case__\": 1, \"filter_config\": {\"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cond_rg\": {\"select_rg\": \"no\", \"__current_case__\": 0}, \"quality\": null, \"library\": null, \"cigarcons\": null, \"inclusive_filter\": null, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"tag\": null, \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"target\", \"__current_case__\": 1, \"target\": {\"__class__\": \"ConnectedValue\"}, \"seed\": \"1\"}}, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"complementary_output\": false, \"adv_output\": {\"readtags\": [], \"collapsecigar\": false}, \"output_format\": {\"oformat\": \"bam\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.15.1+galaxy2", + "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"selected_reads\", \"__current_case__\": 1, \"filter_config\": {\"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cond_rg\": {\"select_rg\": \"no\", \"__current_case__\": 0}, \"cond_expr\": {\"select_expr\": \"no\", \"__current_case__\": 0}, \"quality\": null, \"library\": null, \"cigarcons\": null, \"inclusive_filter\": null, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"tag\": null, \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"target\", \"__current_case__\": 1, \"target\": {\"__class__\": \"ConnectedValue\"}, \"seed\": \"1\"}}, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"complementary_output\": false, \"adv_output\": {\"readtags\": [], \"collapsecigar\": false}, \"output_format\": {\"oformat\": \"bam\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.20+galaxy3", "type": "tool", "uuid": "ae46e826-d985-4437-abae-152b6877eea7", "when": null, @@ -1136,7 +1136,7 @@ }, "22": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "errors": null, "id": 22, "input_connections": { @@ -1153,13 +1153,13 @@ "label": "multiQC", "name": "MultiQC", "outputs": [ - { - "name": "stats", - "type": "input" - }, { "name": "html_report", "type": "html" + }, + { + "name": "stats", + "type": "tabular" } ], "position": { @@ -1173,15 +1173,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "abfd8a6544d7", + "changeset_revision": "f7e2f1eb3a16", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.11+galaxy1", + "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "f7d74248-16e3-4020-8156-caae0e7682ef", "when": null, @@ -1313,7 +1313,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" diff --git a/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-sr.ga b/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-sr.ga index 05c3c38a5..857414f3b 100644 --- a/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-sr.ga +++ b/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-sr.ga @@ -81,7 +81,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "1.1", + "release": "1.2", "name": "Get Confident Peaks From ChIP_SR replicates", "steps": { "0": { @@ -194,7 +194,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "errors": null, "id": 4, "input_connections": { @@ -223,15 +223,15 @@ "output_name": "outputcnt" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "tool_shed_repository": { - "changeset_revision": "6be888be75f9", + "changeset_revision": "32dc5f781059", "name": "samtools_view", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"all_reads\", \"__current_case__\": 0, \"output_options\": {\"reads_report_type\": \"count\", \"__current_case__\": 1}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.15.1+galaxy2", + "tool_version": "1.20+galaxy3", "type": "tool", "uuid": "a864ff43-af08-436a-aa78-54491ff0cce6", "when": null, @@ -841,7 +841,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -944,7 +944,7 @@ }, "19": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "errors": null, "id": 19, "input_connections": { @@ -977,15 +977,15 @@ "output_name": "outputsam" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "tool_shed_repository": { - "changeset_revision": "6be888be75f9", + "changeset_revision": "32dc5f781059", "name": "samtools_view", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"selected_reads\", \"__current_case__\": 1, \"filter_config\": {\"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cond_rg\": {\"select_rg\": \"no\", \"__current_case__\": 0}, \"quality\": null, \"library\": null, \"cigarcons\": null, \"inclusive_filter\": null, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"tag\": null, \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"target\", \"__current_case__\": 1, \"target\": {\"__class__\": \"ConnectedValue\"}, \"seed\": \"1\"}}, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"complementary_output\": false, \"adv_output\": {\"readtags\": [], \"collapsecigar\": false}, \"output_format\": {\"oformat\": \"bam\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.15.1+galaxy2", + "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"selected_reads\", \"__current_case__\": 1, \"filter_config\": {\"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cond_rg\": {\"select_rg\": \"no\", \"__current_case__\": 0}, \"cond_expr\": {\"select_expr\": \"no\", \"__current_case__\": 0}, \"quality\": null, \"library\": null, \"cigarcons\": null, \"inclusive_filter\": null, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"tag\": null, \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"target\", \"__current_case__\": 1, \"target\": {\"__class__\": \"ConnectedValue\"}, \"seed\": \"1\"}}, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"complementary_output\": false, \"adv_output\": {\"readtags\": [], \"collapsecigar\": false}, \"output_format\": {\"oformat\": \"bam\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.20+galaxy3", "type": "tool", "uuid": "ae46e826-d985-4437-abae-152b6877eea7", "when": null, @@ -1136,7 +1136,7 @@ }, "22": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "errors": null, "id": 22, "input_connections": { @@ -1153,13 +1153,13 @@ "label": "multiQC", "name": "MultiQC", "outputs": [ - { - "name": "stats", - "type": "input" - }, { "name": "html_report", "type": "html" + }, + { + "name": "stats", + "type": "tabular" } ], "position": { @@ -1173,15 +1173,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "abfd8a6544d7", + "changeset_revision": "f7e2f1eb3a16", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.11+galaxy1", + "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "f7d74248-16e3-4020-8156-caae0e7682ef", "when": null, @@ -1313,7 +1313,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" diff --git a/workflows/epigenetics/cutandrun/CHANGELOG.md b/workflows/epigenetics/cutandrun/CHANGELOG.md index 99a77c9c8..90d5cbc5f 100644 --- a/workflows/epigenetics/cutandrun/CHANGELOG.md +++ b/workflows/epigenetics/cutandrun/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.13] 2024-09-23 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0` + ## [0.12] 2024-07-15 ### Automatic update diff --git a/workflows/epigenetics/cutandrun/cutandrun-tests.yml b/workflows/epigenetics/cutandrun/cutandrun-tests.yml index 8f2ebcecb..3e7e189de 100644 --- a/workflows/epigenetics/cutandrun/cutandrun-tests.yml +++ b/workflows/epigenetics/cutandrun/cutandrun-tests.yml @@ -46,13 +46,15 @@ MACS2 summits: element_tests: Rep1: - has_n_lines: - n: 1856 + asserts: + has_n_lines: + n: 5870 MACS2 narrowPeak: element_tests: Rep1: - has_n_lines: - n: 1856 + asserts: + has_n_lines: + n: 5870 MACS2 peaks xls: element_tests: Rep1: @@ -109,13 +111,15 @@ MACS2 summits: element_tests: Rep1: - has_n_lines: - n: 3261 + asserts: + has_n_lines: + n: 3231 MACS2 narrowPeak: element_tests: Rep1: - has_n_lines: - n: 3261 + asserts: + has_n_lines: + n: 3231 MACS2 peaks xls: element_tests: Rep1: diff --git a/workflows/epigenetics/cutandrun/cutandrun.ga b/workflows/epigenetics/cutandrun/cutandrun.ga index 570a20325..5f8a1fcb6 100644 --- a/workflows/epigenetics/cutandrun/cutandrun.ga +++ b/workflows/epigenetics/cutandrun/cutandrun.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.12", + "release": "0.13", "name": "CUTandRUN", "steps": { "0": { @@ -177,7 +177,7 @@ }, "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "errors": null, "id": 6, "input_connections": { @@ -235,15 +235,15 @@ "output_name": "report" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "aa784cb3810d", + "changeset_revision": "5eb7e84243f2", "name": "cutadapt", "owner": "lparsons", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"adapter_options\": {\"action\": \"trim\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"minimum_length2\": null, \"maximum_length\": null, \"maximum_length2\": null, \"max_n\": null, \"max_expected_errors\": null, \"max_average_error_rate\": null, \"discard_casava\": false, \"pair_filter\": \"any\"}, \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Please use: For R1: - For TrueSeq (CUT and RUN): GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC - For Nextera (CUT and TAG): CTGTCTCTTATACACATCTCCGAGCCCACGAGAC \", \"adapter\": {\"__class__\": \"ConnectedValue\"}}, \"single_noindels\": false}], \"front_adapters\": [], \"anywhere_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Please use: For R2: - For TruSeq (CUT and RUN): GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT - For Nextera (CUT and TAG): CTGTCTCTTATACACATCTGACGCTGCCGACGA\", \"adapter\": {\"__class__\": \"ConnectedValue\"}}, \"single_noindels\": false}], \"front_adapters2\": [], \"anywhere_adapters2\": []}, \"pair_adapters\": false}, \"other_trimming_options\": {\"cut\": \"0\", \"cut2\": \"0\", \"quality_cutoff\": \"30\", \"quality_cutoff2\": \"\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"poly_a\": false, \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"shorten_options_r2\": {\"shorten_values_r2\": \"False\", \"__current_case__\": 1}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"strip_suffix\": \"\", \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.9+galaxy0", + "tool_version": "4.9+galaxy1", "type": "tool", "uuid": "774b0604-628f-46a1-9088-a59d082e5317", "when": null, @@ -698,7 +698,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -765,7 +765,7 @@ }, "14": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "errors": null, "id": 14, "input_connections": { @@ -790,10 +790,6 @@ "label": "MultiQC", "name": "MultiQC", "outputs": [ - { - "name": "stats", - "type": "input" - }, { "name": "plots", "type": "input" @@ -801,6 +797,10 @@ { "name": "html_report", "type": "html" + }, + { + "name": "stats", + "type": "tabular" } ], "position": { @@ -814,15 +814,15 @@ "output_name": "plots" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "abfd8a6544d7", + "changeset_revision": "f7e2f1eb3a16", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"bowtie2\", \"__current_case__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}, {\"__index__\": 3, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.11+galaxy1", + "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"bowtie2\", \"__current_case__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}, {\"__index__\": 3, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "0edf5e04-cc38-414c-9b57-117e919c435b", "when": null, diff --git a/workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler-tests.yml b/workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler-tests.yml index 173062097..27a590032 100644 --- a/workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler-tests.yml +++ b/workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler-tests.yml @@ -81,7 +81,6 @@ value: 47830 delta: 4000 plot with pyGenomeTracks: - class: File file: test-data/plot_chic.png compare: sim_size delta: 1500 diff --git a/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml index 95a438d6b..186fbb60f 100644 --- a/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml +++ b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml @@ -79,7 +79,6 @@ value: 149349 delta: 10000 plot with pyGenomeTracks: - class: File file: test-data/plot_hic.png compare: sim_size delta: 1500 diff --git a/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md b/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md index 93fd2a18b..d04f8127b 100644 --- a/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md +++ b/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md @@ -1,5 +1,17 @@ # Changelog +## [1.1.3] 2024-09-30 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0` + +## [1.1.2] 2024-09-19 + +### Manual update + +- Updated the tool versions manually in the ToolDistillator parameters + ## [1.1.1] 2024-07-08 ### Automatic update diff --git a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly-tests.yml b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly-tests.yml index b184f0a50..8f9012b89 100644 --- a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly-tests.yml +++ b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly-tests.yml @@ -10,41 +10,41 @@ filetype: fastqsanger.gz outputs: shovill_contigs_graph: - assert: - has_n_lines: - n: 18 + asserts: + has_text: + text: "KC:i" shovill_logfile: - assert: + asserts: has_text: text: "[shovill] Done." shovill_contigs_fasta: - assert: + asserts: has_text: text: ">contig00001" quast_report_tabular: - assert: + asserts: has_n_columns: n: 2 has_text: text: "shovill_contigs_fasta" quast_log: - assert: + asserts: has_text: text: "Thank you for using QUAST!" refseqmasher_report_tabular: - assert: + asserts: has_text: text: "Enterococcus faecalis" has_n_columns: n: 21 bandage_contig_graph_stats: - assert: + asserts: has_text: text: "Total length orphaned nodes (bp):" has_n_columns: n: 2 tooldistillator_summarize: - assert: + asserts: has_text: text: "\"Assembly\": \"shovill_contigs_fasta\"" has_text: diff --git a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga index f75417bac..162b4d1b5 100644 --- a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga +++ b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga @@ -26,7 +26,7 @@ } ], "format-version": "0.1", - "release": "1.1.1", + "release": "1.1.3", "license": "GPL-3.0-or-later", "name": "Bacterial Genome Assembly using Shovill", "steps": { @@ -557,7 +557,7 @@ }, "7": { "annotation": "ToolDistillator extracts results from tools and creates a JSON file for each tool", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0", "errors": null, "id": 7, "input_connections": { @@ -623,15 +623,15 @@ "output_name": "output_json" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "a7387ce2a8ca", + "changeset_revision": "8d6686664021", "name": "tooldistillator", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"log\": false, \"tool_section\": {\"tools\": [{\"__index__\": 0, \"select_tool\": {\"tool_list\": \"shovill\", \"__current_case__\": 19, \"input\": {\"__class__\": \"ConnectedValue\"}, \"contig_graph_path\": {\"__class__\": \"ConnectedValue\"}, \"bam_file_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"1.1.0\", \"reference_database_version\": null}}, {\"__index__\": 1, \"select_tool\": {\"tool_list\": \"quast\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}, \"quast_html_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"5.2.0\", \"reference_database_version\": null}}, {\"__index__\": 2, \"select_tool\": {\"tool_list\": \"refseqmasher\", \"__current_case__\": 18, \"input\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"0.1.2\", \"reference_database_version\": null}}, {\"__index__\": 3, \"select_tool\": {\"tool_list\": \"bandage\", \"__current_case__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}, \"bandage_plot_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"0.8.1\", \"reference_database_version\": null}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.9+galaxy0", + "tool_state": "{\"log\": false, \"tool_section\": {\"tools\": [{\"__index__\": 0, \"select_tool\": {\"tool_list\": \"shovill\", \"__current_case__\": 19, \"input\": {\"__class__\": \"ConnectedValue\"}, \"contig_graph_path\": {\"__class__\": \"ConnectedValue\"}, \"bam_file_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"1.1.0\", \"reference_database_version\": null}}, {\"__index__\": 1, \"select_tool\": {\"tool_list\": \"quast\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}, \"quast_html_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"5.2.0\", \"reference_database_version\": null}}, {\"__index__\": 2, \"select_tool\": {\"tool_list\": \"refseqmasher\", \"__current_case__\": 18, \"input\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"0.1.2\", \"reference_database_version\": null}}, {\"__index__\": 3, \"select_tool\": {\"tool_list\": \"bandage\", \"__current_case__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}, \"bandage_plot_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"2022.09\", \"reference_database_version\": null}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.9.1+galaxy0", "type": "tool", "uuid": "b6156c8e-5048-41e3-90d9-f9302734c3d1", "when": null, @@ -645,7 +645,7 @@ }, "8": { "annotation": "ToolDistillator summarize groups all JSON file into a unique JSON file", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0", "errors": null, "id": 8, "input_connections": { @@ -683,15 +683,15 @@ "output_name": "summary_json" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "def7a82d23e1", + "changeset_revision": "f3233d395549", "name": "tooldistillator_summarize", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"summarize_data\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.9+galaxy0", + "tool_version": "0.9.1+galaxy0", "type": "tool", "uuid": "3bbe0eba-b6bb-4d43-ab57-2b899b8112ae", "when": null, diff --git a/workflows/genome-assembly/quality-and-contamination-control/CHANGELOG.md b/workflows/genome-assembly/quality-and-contamination-control/CHANGELOG.md index 41a1d7812..a19c83e30 100644 --- a/workflows/genome-assembly/quality-and-contamination-control/CHANGELOG.md +++ b/workflows/genome-assembly/quality-and-contamination-control/CHANGELOG.md @@ -1,5 +1,27 @@ # Changelog +## [1.1.3] 2024-09-30 + +### Manual update + +- Updated Recentrifuge version manually in the ToolDistillator parameters + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.14.1+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.15.0+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0` + +## [1.1.2] 2024-08-05 + +### Manual update + +- Updated the tool versions manually in the ToolDistillator parameters + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.0+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.14.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.14.1+galaxy0` + ## [1.1.1] 2024-07-08 ### Automatic update diff --git a/workflows/genome-assembly/quality-and-contamination-control/quality_and_contamination_control-tests.yml b/workflows/genome-assembly/quality-and-contamination-control/quality_and_contamination_control-tests.yml index b5768ad0b..adbe029d5 100644 --- a/workflows/genome-assembly/quality-and-contamination-control/quality_and_contamination_control-tests.yml +++ b/workflows/genome-assembly/quality-and-contamination-control/quality_and_contamination_control-tests.yml @@ -12,52 +12,52 @@ Select a NCBI taxonomy database: "2022-03-08" outputs: fastp_report_json: - assert: + asserts: has_text: text: "fastp_version" has_text: text: "read2_before_filtering" kraken_report_tabular: - assert: + asserts: has_text: text: "Enterococcus avium" - has_n_column: + has_n_columns: n: 6 kraken_report_reads: - assert: + asserts: has_text: text: "M07044:90:000000000-JRJWP:1:1119:23974:4461" - has_n_column: + has_n_columns: n: 5 bracken_kraken_report: - assert: + asserts: has_text: text: "Enterococcus gallinarum" - has_n_column: + has_n_columns: n: 6 bracken_report_tsv: - assert: + asserts: has_text: text: "Escherichia coli" - has_n_column: + has_n_columns: n: 7 recentrifuge_data_tabular: - assert: + asserts: has_text: text: "Enterococcus faecalis" - has_n_column: + has_n_columns: n: 6 recentrifuge_stats_tabular: - assert: + asserts: has_text: text: "input_dir/kraken_report_reads" - has_n_column: + has_n_columns: n: 2 tooldistillator_summarize: - assert: - has_text: + asserts: + - that: has_text text: "fastp_report" - has_text: + - that: has_text text: "ncbi_taxonomic_id" - has_text: + - that: has_text text: "kraken2_report" diff --git a/workflows/genome-assembly/quality-and-contamination-control/quality_and_contamination_control.ga b/workflows/genome-assembly/quality-and-contamination-control/quality_and_contamination_control.ga index 8d3ac74fb..6e8b6ea7e 100644 --- a/workflows/genome-assembly/quality-and-contamination-control/quality_and_contamination_control.ga +++ b/workflows/genome-assembly/quality-and-contamination-control/quality_and_contamination_control.ga @@ -27,7 +27,7 @@ ], "format-version": "0.1", "license": "GPL-3.0-or-later", - "release": "1.1.1", + "release": "1.1.3", "name": "Quality and Contamination Control For Genome Assembly", "steps": { "0": { @@ -131,7 +131,7 @@ "top": 454.91066885428484 }, "tool_id": null, - "tool_state": "{\"default\": \"ncbi-2015-10-05\", \"restrictions\": [\"ncbi-2015-10-05\"], \"parameter_type\": \"text\", \"optional\": true}", + "tool_state": "{\"default\": \"ncbi-2015-10-05\", \"restrictions\": [\"ncbi-2015-10-05\", \"2020-12-03\", \"2022-03-08\", \"2024-06-05\"], \"parameter_type\": \"text\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "daac0634-bcf4-4fdd-bcd2-67247f5afdd0", @@ -140,7 +140,7 @@ }, "4": { "annotation": "fastp_triming, quality analaysis and read cleaning", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1", "errors": null, "id": 4, "input_connections": { @@ -259,15 +259,15 @@ "output_name": "report_json" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1", "tool_shed_repository": { - "changeset_revision": "c59d48774d03", + "changeset_revision": "d60c3f704da0", "name": "fastp", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": null, \"umi_len\": null, \"umi_prefix\": null}, \"cutting_by_quality_options\": {\"cut_by_quality5\": false, \"cut_by_quality3\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"paired\", \"__current_case__\": 1, \"in1\": {\"__class__\": \"ConnectedValue\"}, \"in2\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": null, \"adapter_sequence2\": null}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.23.4+galaxy0", + "tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": null, \"umi_len\": null, \"umi_prefix\": null}, \"cutting_by_quality_options\": {\"cut_by_quality5\": false, \"cut_by_quality3\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"paired\", \"__current_case__\": 1, \"in1\": {\"__class__\": \"ConnectedValue\"}, \"in2\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": null, \"adapter_sequence2\": null, \"detect_adapter_for_pe\": false}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.23.4+galaxy1", "type": "tool", "uuid": "7f405009-2491-4633-b4e1-ca0fdbd8360d", "when": null, @@ -396,7 +396,7 @@ }, "6": { "annotation": "bracken_abundance_estimation", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.0+galaxy0", "errors": null, "id": 6, "input_connections": { @@ -456,15 +456,15 @@ "output_name": "report" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.0+galaxy0", "tool_shed_repository": { - "changeset_revision": "1d4bd12f01cf", + "changeset_revision": "0c7b6eb7e752", "name": "bracken", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"kmer_distr\": {\"__class__\": \"ConnectedValue\"}, \"level\": \"S\", \"logfile_output\": false, \"out_report\": true, \"threshold\": \"10\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.9+galaxy0", + "tool_version": "3.0+galaxy0", "type": "tool", "uuid": "e088cdc6-d79b-453c-8787-6d4b7004312a", "when": null, @@ -483,7 +483,7 @@ }, "7": { "annotation": "recentrifuge_taxonomy_visualization", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.14.0+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.15.0+galaxy0", "errors": null, "id": 7, "input_connections": { @@ -584,15 +584,15 @@ "output_name": "stat_tsv" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.14.0+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.15.0+galaxy0", "tool_shed_repository": { - "changeset_revision": "76bf12b928f4", + "changeset_revision": "591175c0f051", "name": "recentrifuge", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"advanced_option\": {\"controls\": \"0\", \"scoring\": null, \"minscore_value\": \"0\", \"mintaxa\": \"0\", \"exclude_taxa_name\": null, \"include_taxa_name\": null, \"avoidcross\": false}, \"database\": {\"database_name\": {\"__class__\": \"ConnectedValue\"}}, \"file_type\": {\"filetype\": \"kraken\", \"__current_case__\": 3}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"more_advanced_option\": {\"ctrlminscore\": \"0\", \"ctrlmintaxa\": \"0\", \"summary\": \"ADD\", \"takeoutroot\": false, \"nokollapse\": false, \"strain\": true, \"sequential\": false}, \"output_option\": {\"extra\": \"TSV\", \"nohtml\": false, \"no_logfile\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.14.0+galaxy0", + "tool_version": "1.15.0+galaxy0", "type": "tool", "uuid": "2db5d20e-62c7-43ad-b21f-e9992c77faa1", "when": null, @@ -621,7 +621,7 @@ }, "8": { "annotation": "ToolDistillator extracts results from tools and creates a JSON file for each tool", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0", "errors": null, "id": 8, "input_connections": { @@ -711,15 +711,15 @@ "output_name": "output_json" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "a7387ce2a8ca", + "changeset_revision": "8d6686664021", "name": "tooldistillator", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"log\": false, \"tool_section\": {\"tools\": [{\"__index__\": 0, \"select_tool\": {\"tool_list\": \"fastp\", \"__current_case__\": 6, \"input\": {\"__class__\": \"ConnectedValue\"}, \"trimmed_forward_R1_path\": {\"__class__\": \"ConnectedValue\"}, \"trimmed_reverse_R2_path\": {\"__class__\": \"ConnectedValue\"}, \"html_report_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"0.23.2\", \"reference_database_version\": null}}, {\"__index__\": 1, \"select_tool\": {\"tool_list\": \"kraken2\", \"__current_case__\": 12, \"input\": {\"__class__\": \"ConnectedValue\"}, \"seq_classification_file_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"2.1.1\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"select_tool\": {\"tool_list\": \"bracken\", \"__current_case__\": 4, \"input\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"2.8\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}, \"kraken_report_path\": {\"__class__\": \"ConnectedValue\"}, \"threshold\": null, \"read_len\": \"100\", \"level\": \"S\"}}, {\"__index__\": 3, \"select_tool\": {\"tool_list\": \"recentrifuge\", \"__current_case__\": 17, \"input\": {\"__class__\": \"ConnectedValue\"}, \"rcf_stat_path\": {\"__class__\": \"ConnectedValue\"}, \"rcf_html_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"1.12.1\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.9+galaxy0", + "tool_state": "{\"log\": false, \"tool_section\": {\"tools\": [{\"__index__\": 0, \"select_tool\": {\"tool_list\": \"fastp\", \"__current_case__\": 6, \"input\": {\"__class__\": \"ConnectedValue\"}, \"trimmed_forward_R1_path\": {\"__class__\": \"ConnectedValue\"}, \"trimmed_reverse_R2_path\": {\"__class__\": \"ConnectedValue\"}, \"html_report_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"0.23.4\", \"reference_database_version\": null}}, {\"__index__\": 1, \"select_tool\": {\"tool_list\": \"kraken2\", \"__current_case__\": 12, \"input\": {\"__class__\": \"ConnectedValue\"}, \"seq_classification_file_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"2.1.3\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"select_tool\": {\"tool_list\": \"bracken\", \"__current_case__\": 4, \"input\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"3.0\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}, \"kraken_report_path\": {\"__class__\": \"ConnectedValue\"}, \"threshold\": null, \"read_len\": \"100\", \"level\": \"S\"}}, {\"__index__\": 3, \"select_tool\": {\"tool_list\": \"recentrifuge\", \"__current_case__\": 17, \"input\": {\"__class__\": \"ConnectedValue\"}, \"rcf_stat_path\": {\"__class__\": \"ConnectedValue\"}, \"rcf_html_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"1.15.0\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.9.1+galaxy0", "type": "tool", "uuid": "b88b0ffe-f660-43ea-b00a-40ca0087f83f", "when": null, @@ -733,7 +733,7 @@ }, "9": { "annotation": "ToolDistillator summarize groups all JSON file into a unique JSON file", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0", "errors": null, "id": 9, "input_connections": { @@ -771,15 +771,15 @@ "output_name": "summary_json" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "def7a82d23e1", + "changeset_revision": "f3233d395549", "name": "tooldistillator_summarize", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"summarize_data\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.9+galaxy0", + "tool_version": "0.9.1+galaxy0", "type": "tool", "uuid": "fbc8d552-c0b1-426c-b26f-8bfe8371b05e", "when": null, diff --git a/workflows/proteomics/clinicalmp/clinicalmp-quantitation/.dockstore.yml b/workflows/proteomics/clinicalmp/clinicalmp-quantitation/.dockstore.yml new file mode 100644 index 000000000..697c2b99f --- /dev/null +++ b/workflows/proteomics/clinicalmp/clinicalmp-quantitation/.dockstore.yml @@ -0,0 +1,11 @@ +version: 1.2 +workflows: +- name: main + subclass: Galaxy + publish: true + primaryDescriptorPath: /iwc-clinicalmp-quantitation.ga + testParameterFiles: + - /iwc-clinicalmp-quantitation-tests.yml + authors: + - name: GalaxyP + url: https://galaxyp.org/ diff --git a/workflows/proteomics/clinicalmp/clinicalmp-quantitation/README.md b/workflows/proteomics/clinicalmp/clinicalmp-quantitation/README.md new file mode 100644 index 000000000..76677fcf2 --- /dev/null +++ b/workflows/proteomics/clinicalmp/clinicalmp-quantitation/README.md @@ -0,0 +1,25 @@ +# Clinical Metaproteomics 4: Quantitation + +Quantitative proteomics is crucial for many important purposes. It allows researchers to measure and compare the levels of proteins or peptides in biological samples. This provides valuable insights into biomarker discovery, comparative analysis, and differential expression studies. Quantitative proteomics also helps in understanding the functional roles of proteins, the composition of protein complexes, and the effects of drugs on protein expression in pharmacological studies. Additionally, it serves as a quality control measure by validating initial protein identifications and providing data normalization for increased accuracy. The quantitative data are essential for hypothesis testing, and systems biology, and have clinical relevance in areas such as disease diagnosis, prognosis, and therapeutic decision-making. In summary, the quantitation workflow in proteomics is essential for understanding the complexities of protein expression and regulation, and it facilitates a wide range of biological and clinical applications. + +In this current workflow, we perform Quantification using the MaxQuant tool. A GTN has been developed for this workflow. +https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-4-quantitation/tutorial.html + +## Inputs dataset + +- `RAW MSMS datasets` in RAW dataset collection +- `Quantitation_Database_for_MaxQuant` in Fasta (protein sequences for database searching) +- `Experimental-Design Discovery MaxQuant` in Tabular Format + +## Inputs values + +For MaxQuant +- Peptide Length +- Variable modifications +- Labeled element + + +## Processing + +- extract microbial proteins and peptides using Select and Cut +- Grouping duplicates using the Group tool diff --git a/workflows/proteomics/clinicalmp/clinicalmp-quantitation/iwc-clinicalmp-quantitation-tests.yml b/workflows/proteomics/clinicalmp/clinicalmp-quantitation/iwc-clinicalmp-quantitation-tests.yml new file mode 100644 index 000000000..53fbca031 --- /dev/null +++ b/workflows/proteomics/clinicalmp/clinicalmp-quantitation/iwc-clinicalmp-quantitation-tests.yml @@ -0,0 +1,31 @@ +- doc: Test outline for iwc-clinicalmp-quantitation + job: + Quantitation_Database-For-MaxQuant: + class: File + location: https://zenodo.org/records/10720030/files/Quantitation_Database_for_MaxQuant.fasta + filetype: fasta + Experimental-Design Discovery MaxQuant: + class: File + location: https://zenodo.org/records/10720030/files/Experimental-Design_Discovery_MaxQuant.tabular + filetype: tabular + Input Raw-files: + class: Collection + collection_type: list + elements: + - class: File + identifier: PTRC_Skubitz_Plex2_F15_9Aug19_Rage_Rep-19-06-08.raw + location: https://zenodo.org/records/10720030/files/PTRC_Skubitz_Plex2_F15_9Aug19_Rage_Rep-19-06-08.raw + - class: File + identifier: PTRC_Skubitz_Plex2_F13_9Aug19_Rage_Rep-19-06-08.raw + location: https://zenodo.org/records/10720030/files/PTRC_Skubitz_Plex2_F13_9Aug19_Rage_Rep-19-06-08.raw + - class: File + identifier: PTRC_Skubitz_Plex2_F11_9Aug19_Rage_Rep-19-06-08.raw + location: https://zenodo.org/records/10720030/files/PTRC_Skubitz_Plex2_F11_9Aug19_Rage_Rep-19-06-08.raw + - class: File + identifier: PTRC_Skubitz_Plex2_F10_9Aug19_Rage_Rep-19-06-08.raw + location: https://zenodo.org/records/10720030/files/PTRC_Skubitz_Plex2_F10_9Aug19_Rage_Rep-19-06-08.raw + outputs: + Quantified-Proteins: + path: test-data/Quantified-Proteins.tabular + Quantified-Peptides: + path: test-data/Quantified-Peptides.tabular diff --git a/workflows/proteomics/clinicalmp/clinicalmp-quantitation/iwc-clinicalmp-quantitation.ga b/workflows/proteomics/clinicalmp/clinicalmp-quantitation/iwc-clinicalmp-quantitation.ga new file mode 100644 index 000000000..9021d3f8a --- /dev/null +++ b/workflows/proteomics/clinicalmp/clinicalmp-quantitation/iwc-clinicalmp-quantitation.ga @@ -0,0 +1,404 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "Clinical Metaproteomics 4: Quantitation ", + "comments": [], + "creator": [ + { + "class": "Organization", + "name": "GalaxyP" + } + ], + "format-version": "0.1", + "license": "CC-BY-4.0", + "name": "Clinical Metaproteomics Quantitation", + "release": "0.1", + "report": { + "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" + }, + "steps": { + "0": { + "annotation": "Input protein database", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "Input protein database", + "name": "Quantitation_Database-For-MaxQuant" + } + ], + "label": "Quantitation_Database-For-MaxQuant", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 0, + "top": 0 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "c2311b55-b0c7-4237-bed1-4b25bf1a1655", + "when": null, + "workflow_outputs": [] + }, + "1": { + "annotation": "design file ", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "design file ", + "name": "Experimental-Design Discovery MaxQuant" + } + ], + "label": "Experimental-Design Discovery MaxQuant", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 65.796875, + "top": 168.203125 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "d957f00d-79a9-4e2e-8e15-088444ca5605", + "when": null, + "workflow_outputs": [] + }, + "2": { + "annotation": "MSMS data", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "MSMS data", + "name": "Input Raw-files" + } + ], + "label": "Input Raw-files", + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 41.671875, + "top": 532.3671875 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "2864b493-6d12-4313-ad29-f3b1e2564aba", + "when": null, + "workflow_outputs": [] + }, + "3": { + "annotation": "Database searching", + "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/2.0.3.0+galaxy0", + "errors": null, + "id": 3, + "input_connections": { + "input_opts|fasta_files": { + "id": 0, + "output_name": "output" + }, + "paramGroups_0|files": { + "id": 2, + "output_name": "output" + }, + "search_opts|template": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool MaxQuant", + "name": "input_opts" + }, + { + "description": "runtime parameter for tool MaxQuant", + "name": "search_opts" + } + ], + "label": "MaxQuant", + "name": "MaxQuant", + "outputs": [ + { + "name": "proteinGroups", + "type": "tabular" + }, + { + "name": "mqpar", + "type": "xml" + }, + { + "name": "peptides", + "type": "tabular" + }, + { + "name": "evidence", + "type": "tabular" + }, + { + "name": "msms", + "type": "tabular" + } + ], + "position": { + "left": 427.9609375, + "top": 170.17578125 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/2.0.3.0+galaxy0", + "tool_shed_repository": { + "changeset_revision": "9c52362ae7bb", + "name": "maxquant", + "owner": "galaxyp", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"input_opts\": {\"ftype\": \".thermo.raw\", \"fasta_files\": {\"__class__\": \"ConnectedValue\"}, \"identifier_parse_rule\": \">([^\\\\s]*)\", \"description_parse_rule\": \">(.*)\"}, \"output_opts\": {\"dry_run\": false, \"output\": [\"proteinGroups\", \"mqpar\", \"peptides\", \"msms\", \"evidence\"]}, \"paramGroups\": [{\"__index__\": 0, \"files\": {\"__class__\": \"ConnectedValue\"}, \"maxMissedCleavages\": \"2\", \"fixedModifications\": [\"Carbamidomethyl (C)\"], \"variableModifications\": [\"Oxidation (M)\"], \"enzymes\": [\"Trypsin/P\"], \"digestion_mode\": \"0\", \"quant_method\": {\"select_quant_method\": \"reporter_ion_ms2\", \"__current_case__\": 3, \"iso_labels\": {\"labeling\": \"tmt11plex\", \"__current_case__\": 4}, \"filter_by_pif\": {\"filter_pif\": \"False\", \"__current_case__\": 1}}}], \"protein_quant\": {\"peptides_for_quantification\": \"1\", \"only_unmod_prot\": {\"unmod_prot\": \"True\", \"__current_case__\": 0, \"mods_used_prot_quant\": [\"Oxidation (M)\"], \"discard_unmod_cpart_peptides\": true}, \"lfq_opts\": {\"separateLfq\": false, \"lfqStabilizeLargeRatios\": true, \"lfqRequireMsms\": true, \"do_ibaq\": {\"ibaq\": \"False\", \"__current_case__\": 1}, \"advancedSiteIntensities\": true}}, \"qc\": {\"do_it\": \"false\", \"__current_case__\": 1}, \"search_opts\": {\"template\": {\"__class__\": \"ConnectedValue\"}, \"min_peptide_len\": \"8\", \"max_peptide_mass\": \"4600\", \"min_unique_pep\": \"0\", \"calc_peak_properties\": false, \"mbr\": {\"match_between_runs\": \"True\", 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b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/CHANGELOG.md index f43e4eac3..9c87f0a03 100644 --- a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/CHANGELOG.md +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/CHANGELOG.md @@ -1,5 +1,12 @@ # Changelog +## [0.5.3] 2024-10-01 + +### Tool updates + +- `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0` updated to `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy0` updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1` + ## [0.5.2] 2024-03-05 ### Automatic update diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation.ga b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation.ga index 3f1530d61..aaf2b6107 100644 --- a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation.ga +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation.ga @@ -11,7 +11,7 @@ "format-version": "0.1", "license": "MIT", "name": "COVID-19: variation analysis on ARTIC PE data", - "release": "0.5.2", + "release": "0.5.3", "steps": { "0": { "annotation": "Illumina reads from ARTIC assay with fastqsanger encoding", @@ -231,7 +231,7 @@ }, "8": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1", "errors": null, "id": 8, "input_connections": { @@ -273,15 +273,15 @@ "output_name": "report_json" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1", "tool_shed_repository": { - "changeset_revision": "c59d48774d03", + "changeset_revision": "d60c3f704da0", "name": "fastp", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, 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\"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": \"\", \"umi_len\": null, \"umi_prefix\": \"\"}, \"cutting_by_quality_options\": {\"cut_by_quality5\": false, \"cut_by_quality3\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"paired_collection\", \"__current_case__\": 2, \"paired_input\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": \"\", \"adapter_sequence2\": \"\", \"detect_adapter_for_pe\": false}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.23.4+galaxy1", "type": "tool", "uuid": "849d9cac-14b8-4e45-823d-5747709e8b60", "when": null, @@ -1543,7 +1543,7 @@ }, "30": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "errors": null, "id": 30, "input_connections": { @@ -1571,15 +1571,15 @@ "top": 745.546875 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "12615d397df7", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"infile\": {\"__class__\": \"ConnectedValue\"}, \"replacements\": [{\"__index__\": 0, \"find_pattern\": \"^##INFO=\"}, {\"__index__\": 1, \"find_pattern\": \"^##INFO= --min-bq among all bases at the site\\\">\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.3+galaxy0", + "tool_version": "9.3+galaxy1", "type": "tool", "uuid": "490dbabb-04ee-426d-a8e5-e2ec9e59de3a", "when": null, @@ -1731,4 +1731,4 @@ "covid19.galaxyproject.org" ], "uuid": "864427b0-d25a-499c-b437-f83f2d6b83f2" -} \ No newline at end of file +} diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/CHANGELOG.md b/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/CHANGELOG.md index f7f1325f7..166bbf5df 100644 --- a/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/CHANGELOG.md +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/CHANGELOG.md @@ -1,5 +1,14 @@ # Changelog +## [0.3.4] 2024-09-24 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1` + ## [0.3.2] 2023-11-28 ### Automatic update diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/variation-reporting.ga b/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/variation-reporting.ga index ffcbe21e9..10afce516 100644 --- a/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/variation-reporting.ga +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/variation-reporting.ga @@ -11,7 +11,7 @@ "format-version": "0.1", "license": "MIT", "name": "COVID-19: variation analysis reporting", - "release": "0.3.3", + "release": "0.3.4", "steps": { "0": { "annotation": "Variation data in VCF format. Can be the output of any of the workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling", @@ -210,12 +210,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool SnpSift Filter", - "name": "input" - } - ], + "inputs": [], "label": null, "name": "SnpSift Filter", "outputs": [ @@ -382,10 +377,6 @@ { "description": "runtime parameter for tool SnpSift Filter", "name": "filtering" - }, - { - "description": "runtime parameter for tool SnpSift Filter", - "name": "input" } ], "label": null, @@ -440,12 +431,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool SnpSift Extract Fields", - "name": "input" - } - ], + "inputs": [], "label": null, "name": "SnpSift Extract Fields", "outputs": [ @@ -502,16 +488,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Replace column", - "name": "original_file" - }, - { - "description": "runtime parameter for tool Replace column", - "name": "replace_information" - } - ], + "inputs": [], "label": null, "name": "Replace column", "outputs": [ @@ -562,7 +539,7 @@ }, "12": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", "errors": null, "id": 12, "input_connections": { @@ -571,12 +548,7 @@ "output_name": "outfile_replace" } }, - "inputs": [ - { - "description": "runtime parameter for tool Compute", - "name": "input" - } - ], + "inputs": [], "label": null, "name": "Compute", "outputs": [ @@ -598,15 +570,15 @@ "output_name": "out_file1" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", "tool_shed_repository": { - "changeset_revision": "6595517c2dd8", + "changeset_revision": "aff5135563c6", "name": "column_maker", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"yes\", \"__current_case__\": 1, \"expressions\": [{\"__index__\": 0, \"cond\": \"c7\", \"add_column\": {\"mode\": \"I\", \"__current_case__\": 1, \"pos\": \"8\"}, \"new_column_name\": \"AFcaller\"}, {\"__index__\": 1, \"cond\": \"round((c18 + c19) / c6, 6)\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"7\"}, \"new_column_name\": \"AF\"}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.0", + "tool_version": "2.1", "type": "tool", "uuid": "c457f29e-dea5-449a-84c4-4b192da88257", "when": null, @@ -629,12 +601,7 @@ "output_name": "out_file1" } }, - "inputs": [ - { - "description": "runtime parameter for tool Datamash", - "name": "in_file" - } - ], + "inputs": [], "label": null, "name": "Datamash", "outputs": [ @@ -678,7 +645,7 @@ }, "14": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "errors": null, "id": 14, "input_connections": { @@ -687,12 +654,7 @@ "output_name": "out_file" } }, - "inputs": [ - { - "description": "runtime parameter for tool Replace", - "name": "infile" - } - ], + "inputs": [], "label": null, "name": "Replace", "outputs": [ @@ -714,15 +676,15 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "12615d397df7", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\s]+\", \"replace_pattern\": \"\\\\t$1\\\\t$2\\\\t$3\\\\t$4\\\\t$5\\\\t$6\\\\t$7\", \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": true, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}, {\"__index__\": 1, \"find_pattern\": \"(GroupBy|collapse)\\\\(([^)]+)\\\\)\", \"replace_pattern\": \"$2\", \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.3+galaxy0", + "tool_version": "9.3+galaxy1", "type": "tool", "uuid": "25f665b6-2b6a-49a3-a395-29706cd772ab", "when": null, @@ -745,12 +707,7 @@ "output_name": "outfile" } }, - "inputs": [ - { - "description": "runtime parameter for tool Collapse Collection", - "name": "input_list" - } - ], + "inputs": [], "label": null, "name": "Collapse Collection", "outputs": [ @@ -786,7 +743,7 @@ }, "16": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", "errors": null, "id": 16, "input_connections": { @@ -795,12 +752,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Compute", - "name": "input" - } - ], + "inputs": [], "label": null, "name": "Compute", "outputs": [ @@ -820,15 +772,15 @@ "output_name": "out_file1" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", "tool_shed_repository": { - "changeset_revision": "6595517c2dd8", + "changeset_revision": "aff5135563c6", "name": "column_maker", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": false, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"yes\", \"__current_case__\": 1, \"expressions\": [{\"__index__\": 0, \"cond\": \"c5 + '>' + c6\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}, \"new_column_name\": \"change\"}, {\"__index__\": 1, \"cond\": \"c3 + ':' + c19\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}, \"new_column_name\": \"change_with_pos\"}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.0", + "tool_version": "2.1", "type": "tool", "uuid": "cc8a768f-8078-4bdd-ae98-903f08619070", "when": null, @@ -836,7 +788,7 @@ }, "17": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "errors": null, "id": 17, "input_connections": { @@ -845,12 +797,7 @@ "output_name": "out_file1" } }, - "inputs": [ - { - "description": "runtime parameter for tool Replace", - "name": "infile" - } - ], + "inputs": [], "label": null, "name": "Replace", "outputs": [ @@ -872,15 +819,15 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "12615d397df7", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"EFF[*].\", \"replace_pattern\": \"\", \"is_regex\": false, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.3+galaxy0", + "tool_version": "9.3+galaxy1", "type": "tool", "uuid": "82276b6c-5c6e-49eb-8ee5-46041c273d30", "when": null, @@ -903,12 +850,7 @@ "output_name": "outfile" } }, - "inputs": [ - { - "description": "runtime parameter for tool Datamash", - "name": "in_file" - } - ], + "inputs": [], "label": null, "name": "Datamash", "outputs": [ @@ -953,12 +895,7 @@ "output_name": "outfile" } }, - "inputs": [ - { - "description": "runtime parameter for tool Filter", - "name": "input" - } - ], + "inputs": [], "label": null, "name": "Filter", "outputs": [ @@ -997,12 +934,7 @@ "output_name": "outfile" } }, - "inputs": [ - { - "description": "runtime parameter for tool Datamash", - "name": "in_file" - } - ], + "inputs": [], "label": null, "name": "Datamash", "outputs": [ @@ -1045,7 +977,7 @@ }, "21": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1", "errors": null, "id": 21, "input_connections": { @@ -1058,16 +990,7 @@ "output_name": "out_file" } }, - "inputs": [ - { - "description": "runtime parameter for tool Join", - "name": "infile1" - }, - { - "description": "runtime parameter for tool Join", - "name": "infile2" - } - ], + "inputs": [], "label": null, "name": "Join", "outputs": [ @@ -1094,15 +1017,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "12615d397df7", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"column1\": \"20\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": true, \"ignore_case\": false, \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.3+galaxy0", + "tool_version": "9.3+galaxy1", "type": "tool", "uuid": "7e27aac8-1d1e-4d82-88e3-59c4cd61baeb", "when": null, @@ -1119,12 +1042,7 @@ "output_name": "out_file1" } }, - "inputs": [ - { - "description": "runtime parameter for tool Datamash", - "name": "in_file" - } - ], + "inputs": [], "label": null, "name": "Datamash", "outputs": [ @@ -1169,12 +1087,7 @@ "output_name": "out_file1" } }, - "inputs": [ - { - "description": "runtime parameter for tool Datamash", - "name": "in_file" - } - ], + "inputs": [], "label": null, "name": "Datamash", "outputs": [ @@ -1219,12 +1132,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Datamash", - "name": "in_file" - } - ], + "inputs": [], "label": null, "name": "Datamash", "outputs": [ @@ -1260,7 +1168,7 @@ }, "25": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1", "errors": null, "id": 25, "input_connections": { @@ -1273,16 +1181,7 @@ "output_name": "out_file" } }, - "inputs": [ - { - "description": "runtime parameter for tool Join", - "name": "infile1" - }, - { - "description": "runtime parameter for tool Join", - "name": "infile2" - } - ], + "inputs": [], "label": null, "name": "Join", "outputs": [ @@ -1302,15 +1201,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "12615d397df7", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"column1\": \"3\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": true, \"ignore_case\": false, \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.3+galaxy0", + "tool_version": "9.3+galaxy1", "type": "tool", "uuid": "3927af37-c003-4fac-a8af-88ba2b656b22", "when": null, @@ -1318,7 +1217,7 @@ }, "26": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1", "errors": null, "id": 26, "input_connections": { @@ -1331,16 +1230,7 @@ "output_name": "out_file" } }, - "inputs": [ - { - "description": "runtime parameter for tool Join", - "name": "infile1" - }, - { - "description": "runtime parameter for tool Join", - "name": "infile2" - } - ], + "inputs": [], "label": null, "name": "Join", "outputs": [ @@ -1360,15 +1250,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "12615d397df7", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"column1\": \"20\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": true, \"ignore_case\": false, \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.3+galaxy0", + "tool_version": "9.3+galaxy1", "type": "tool", "uuid": "472af513-7900-41a5-b049-feb2d630ad2c", "when": null, @@ -1385,12 +1275,7 @@ "output_name": "out_file" } }, - "inputs": [ - { - "description": "runtime parameter for tool Cut", - "name": "input" - } - ], + "inputs": [], "label": null, "name": "Cut", "outputs": [ @@ -1420,7 +1305,7 @@ }, "28": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1", "errors": null, "id": 28, "input_connections": { @@ -1433,16 +1318,7 @@ "output_name": "out_file" } }, - "inputs": [ - { - "description": "runtime parameter for tool Join", - "name": "infile1" - }, - { - "description": "runtime parameter for tool Join", - "name": "infile2" - } - ], + "inputs": [], "label": null, "name": "Join", "outputs": [ @@ -1469,15 +1345,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "12615d397df7", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"column1\": \"1\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": true, \"ignore_case\": false, \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.3+galaxy0", + "tool_version": "9.3+galaxy1", "type": "tool", "uuid": "1b250a36-d3ae-415e-9764-006182096a60", "when": null, @@ -1494,12 +1370,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Cut", - "name": "input" - } - ], + "inputs": [], "label": null, "name": "Cut", "outputs": [ @@ -1529,7 +1400,7 @@ }, "30": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "errors": null, "id": 30, "input_connections": { @@ -1538,12 +1409,7 @@ "output_name": "out_file1" } }, - "inputs": [ - { - "description": "runtime parameter for tool Replace", - "name": "infile" - } - ], + "inputs": [], "label": null, "name": "Replace", "outputs": [ @@ -1570,15 +1436,15 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "12615d397df7", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"unique\\\\(Sample\\\\)\\\\tcollapse\\\\(Sample\\\\)\\\\tcollapse\\\\(AF\\\\)\", \"replace_pattern\": \"SAMPLES(above-thresholds)\\\\tSAMPLES(all)\\\\tAFs(all)\", \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.3+galaxy0", + "tool_version": "9.3+galaxy1", "type": "tool", "uuid": "6116c1c6-7c7c-43fe-9c91-609c91c6ed85", "when": null, @@ -1595,12 +1461,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Cut", - "name": "input" - } - ], + "inputs": [], "label": null, "name": "Cut", "outputs": [ @@ -1630,7 +1491,7 @@ }, "32": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.1", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", "errors": null, "id": 32, "input_connections": { @@ -1666,15 +1527,15 @@ "output_name": "list_output_tab" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", "tool_shed_repository": { - "changeset_revision": "baabc30154cd", + "changeset_revision": "2dae863c8f42", "name": "split_file_to_collection", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"split_parms\": {\"select_ftype\": \"tabular\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"top\": \"1\", \"split_by\": {\"select_split_by\": \"col\", \"__current_case__\": 0, \"id_col\": \"1\", \"match_regex\": \"(.*)\", \"sub_regex\": \"\\\\1\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.5.1", + "tool_version": "0.5.2", "type": "tool", "uuid": "9f938b6a-e7fb-4509-9c15-271c475092aa", "when": null, @@ -1688,7 +1549,7 @@ }, "33": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1", "errors": null, "id": 33, "input_connections": { @@ -1697,12 +1558,7 @@ "output_name": "outfile" } }, - "inputs": [ - { - "description": "runtime parameter for tool Sort", - "name": "infile" - } - ], + "inputs": [], "label": null, "name": "Sort", "outputs": [ @@ -1724,15 +1580,15 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "12615d397df7", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"header\": \"1\", \"ignore_case\": false, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"sortkeys\": [{\"__index__\": 0, \"column\": \"1\", \"order\": \"\", \"style\": \"g\"}], \"unique\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.3+galaxy0", + "tool_version": "9.3+galaxy1", "type": "tool", "uuid": "0b2f751b-03c6-4302-9060-16856bb4157c", "when": null, @@ -1746,7 +1602,7 @@ }, "34": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1", "errors": null, "id": 34, "input_connections": { @@ -1755,12 +1611,7 @@ "output_name": "out_file1" } }, - "inputs": [ - { - "description": "runtime parameter for tool Sort", - "name": "infile" - } - ], + "inputs": [], "label": null, "name": "Sort", "outputs": [ @@ -1782,15 +1633,15 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "12615d397df7", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"header\": \"1\", \"ignore_case\": false, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"sortkeys\": [{\"__index__\": 0, \"column\": \"1\", \"order\": \"\", \"style\": \"\"}, {\"__index__\": 1, \"column\": \"2\", \"order\": \"\", \"style\": \"n\"}], \"unique\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.3+galaxy0", + "tool_version": "9.3+galaxy1", "type": "tool", "uuid": "e55320de-be51-4fa5-908e-76c03de24a77", "when": null, @@ -1821,10 +1672,6 @@ { "description": "runtime parameter for tool Variant Frequency Plot", "name": "clustering" - }, - { - "description": "runtime parameter for tool Variant Frequency Plot", - "name": "sinputs" } ], "label": null, diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/CHANGELOG.md b/workflows/scRNAseq/fastq-to-matrix-10x/CHANGELOG.md index 9771fe8a1..df831a515 100644 --- a/workflows/scRNAseq/fastq-to-matrix-10x/CHANGELOG.md +++ b/workflows/scRNAseq/fastq-to-matrix-10x/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.5] 2024-09-25 + +### Manual update +- `toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0` + ## [0.4] 2024-04-08 ### Automatic update diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml index eb13dcea9..723587f8b 100644 --- a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml +++ b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml @@ -54,15 +54,11 @@ Number of expected cells: 500 outputs: MultiQC_STARsolo: - class: File asserts: - - that: "has_text_matching" - expression: ">subsample
3[0-9].[0-9]%
33.[0-9]%
" Seurat input for gene expression (filtered): - class: Collection - collection_type: list:list + attributes: { collection_type: list:list } element_tests: subsample: elements: @@ -79,8 +75,7 @@ has_line: line: "FBgn0250732 gfzf" CITE-seq-Count report: - class: Collection - collection_type: list + attributes: { collection_type: list } element_tests: subsample: asserts: @@ -93,8 +88,7 @@ - that: "has_line" line: "Percentage unmapped: 1" Seurat input for CMO (UMI): - class: Collection - collection_type: list:list + attributes: { collection_type: list:list } element_tests: subsample: elements: diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex.ga b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex.ga index 7ea0d5b76..04abdf111 100644 --- a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex.ga +++ b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex.ga @@ -1,6 +1,7 @@ { "a_galaxy_workflow": "true", "annotation": "This workflow processes the CMO fastqs with CITE-seq-Count and include the translation step required for cellPlex processing. In parallel it processes the Gene Expresion fastqs with STARsolo, filter cells with DropletUtils and reformat all outputs to be easily used by the function 'Read10X' from Seurat.", + "comments": [], "creator": [ { "class": "Person", @@ -30,7 +31,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.4", + "release": "0.5", "name": "scRNA-seq_preprocessing_10X_cellPlex", "steps": { "0": { @@ -464,7 +465,7 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1", "errors": null, "id": 5, "input_connections": { @@ -572,15 +573,15 @@ "output_name": "reads_per_gene" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1", "tool_shed_repository": { - "changeset_revision": "42ce70172b72", + "changeset_revision": "45795f582ae9", "name": "rna_starsolo", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"outWig\": {\"outWigType\": \"None\", \"__current_case__\": 0, \"outWigStrand\": \"false\"}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf-with-gtf\", \"__current_case__\": 1, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfile\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfeatureExon\": \"exon\", \"sjdbOverhang\": \"100\"}}, \"sc\": {\"solo_type\": \"CB_UMI_Simple\", \"__current_case__\": 0, \"input_types\": {\"use\": \"list_paired\", \"__current_case__\": 1, \"input_collection\": {\"__class__\": \"ConnectedValue\"}}, \"soloCBwhitelist\": {\"__class__\": \"ConnectedValue\"}, \"params\": {\"chemistry\": \"Cv3\", \"__current_case__\": 1}, \"soloBarcodeReadLength\": {\"__class__\": \"ConnectedValue\"}, \"umidedup\": {\"soloUMIdedup\": \"1MM_CR\", \"__current_case__\": 4, \"soloUMIfiltering\": \"-\"}, \"soloCBmatchWLtype\": \"1MM_multi\"}, \"solo\": {\"soloStrand\": \"Forward\", \"soloFeatures\": \"Gene\", \"filter\": {\"filter_type\": \"no_filter\", \"__current_case__\": 3, \"output_raw\": \"true\"}, \"soloOutFormatFeaturesGeneField3\": \"Gene Expression\", \"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\", \"GX\", \"GN\", \"CB\", \"UB\"], \"quantModeGene\": true, \"outSAMunmapped\": false, \"outSAMmapqUnique\": \"60\", \"junction_limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.7.11a+galaxy0", + "tool_state": "{\"outWig\": {\"outWigType\": \"None\", \"__current_case__\": 0, \"outWigStrand\": \"false\"}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf-with-gtf\", \"__current_case__\": 1, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfile\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfeatureExon\": \"exon\", \"sjdbOverhang\": \"100\"}}, \"sc\": {\"solo_type\": \"CB_UMI_Simple\", \"__current_case__\": 0, \"input_types\": {\"use\": \"list_paired\", \"__current_case__\": 1, \"input_collection\": {\"__class__\": \"ConnectedValue\"}}, \"soloCBwhitelist\": {\"__class__\": \"ConnectedValue\"}, \"params\": {\"chemistry\": \"Cv3\", \"__current_case__\": 1}, \"soloBarcodeReadLength\": {\"__class__\": \"ConnectedValue\"}, \"umidedup\": {\"soloUMIdedup\": \"1MM_CR\", \"__current_case__\": 4, \"soloUMIfiltering\": \"-\"}, \"soloCBmatchWLtype\": \"1MM_multi\"}, \"solo\": {\"soloStrand\": \"Forward\", \"soloFeatures\": \"Gene\", \"wasp_conditional\": {\"waspOutputMode\": \"\", \"__current_case__\": 1}, \"filter\": {\"filter_type\": \"no_filter\", \"__current_case__\": 3, \"output_raw\": \"true\"}, \"soloOutFormatFeaturesGeneField3\": \"Gene Expression\", \"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\", \"GX\", \"GN\", \"CB\", \"UB\"], \"quantModeGene\": true, \"outSAMunmapped\": false, \"outSAMmapqUnique\": \"60\", \"junction_limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.7.11a+galaxy1", "type": "tool", "uuid": "cef740b0-fa95-4542-b08f-dbfca4bfb3e5", "when": null, @@ -588,7 +589,7 @@ }, "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "errors": null, "id": 6, "input_connections": { @@ -605,13 +606,13 @@ "label": "multiQC", "name": "MultiQC", "outputs": [ - { - "name": "stats", - "type": "input" - }, { "name": "html_report", "type": "html" + }, + { + "name": "stats", + "type": "tabular" } ], "position": { @@ -625,15 +626,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "abfd8a6544d7", + "changeset_revision": "f7e2f1eb3a16", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"genecounts\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.11+galaxy1", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "a16bf20e-2bc9-45e7-a0a3-b5590212b973", "when": null, @@ -954,7 +955,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -999,7 +1000,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1044,7 +1045,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1295,8 +1296,8 @@ ] } }, - "tags": "", - "uuid": "89502a02-ec65-400c-b428-68eda7ea6b40" + "tags": [], + "uuid": "933626df-33e9-46ac-8206-d297a7fcb83a" }, "tool_id": null, "type": "subworkflow", @@ -1311,7 +1312,7 @@ ] } }, - "tags": "", + "tags": [], "uuid": "a999ad68-faa9-4ccb-81b4-ac648af028bd" }, "tool_id": null, @@ -1534,7 +1535,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1753,7 +1754,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1798,7 +1799,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1843,7 +1844,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -2094,7 +2095,7 @@ ] } }, - "tags": "", + "tags": [], "uuid": "79342c4e-bb7a-4b25-a214-7d5a10fbfd79" }, "tool_id": null, @@ -2166,6 +2167,6 @@ "tags": [ "#single-cell" ], - "uuid": "b8bd25f7-caa3-44da-8329-26dce6d46636", - "version": 4 + "uuid": "470536e7-ac58-4859-94d6-2085be9c2e17", + "version": 3 } \ No newline at end of file diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3-tests.yml b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3-tests.yml index 82a7c4eee..dcfa61c1d 100644 --- a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3-tests.yml +++ b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3-tests.yml @@ -29,15 +29,11 @@ filetype: tabular outputs: 'MultiQC on input dataset(s): Webpage': - class: File asserts: - - that: "has_text_matching" - expression: ">subsample
3[0-9].[0-9]%
33.[0-9]%
" Seurat input for gene expression (filtered): - class: Collection - collection_type: list:list + attributes: { collection_type: list:list } element_tests: subsample: elements: diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3.ga b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3.ga index 89f7de368..dd5740b2b 100644 --- a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3.ga +++ b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3.ga @@ -30,7 +30,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.4", + "release": "0.5", "name": "scRNA-seq_preprocessing_10X_v3_Bundle", "steps": { "0": { @@ -170,7 +170,7 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1", "errors": null, "id": 5, "input_connections": { @@ -278,15 +278,15 @@ "output_name": "reads_per_gene" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1", "tool_shed_repository": { - "changeset_revision": "42ce70172b72", + "changeset_revision": "45795f582ae9", "name": "rna_starsolo", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"outWig\": {\"outWigType\": \"None\", \"__current_case__\": 0, \"outWigStrand\": \"false\"}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf-with-gtf\", \"__current_case__\": 1, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfile\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfeatureExon\": \"exon\", \"sjdbOverhang\": \"100\"}}, \"sc\": {\"solo_type\": \"CB_UMI_Simple\", \"__current_case__\": 0, \"input_types\": {\"use\": \"list_paired\", \"__current_case__\": 1, \"input_collection\": {\"__class__\": \"ConnectedValue\"}}, \"soloCBwhitelist\": {\"__class__\": \"ConnectedValue\"}, \"params\": {\"chemistry\": \"Cv3\", \"__current_case__\": 1}, \"soloBarcodeReadLength\": {\"__class__\": \"ConnectedValue\"}, \"umidedup\": {\"soloUMIdedup\": \"1MM_CR\", \"__current_case__\": 4, \"soloUMIfiltering\": \"-\"}, \"soloCBmatchWLtype\": \"1MM_multi\"}, \"solo\": {\"soloStrand\": \"Forward\", \"soloFeatures\": \"Gene\", \"filter\": {\"filter_type\": \"no_filter\", \"__current_case__\": 3, \"output_raw\": \"true\"}, \"soloOutFormatFeaturesGeneField3\": \"Gene Expression\", \"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\", \"GX\", \"GN\", \"CB\", \"UB\"], \"quantModeGene\": true, \"outSAMunmapped\": false, \"outSAMmapqUnique\": \"60\", \"junction_limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.7.11a+galaxy0", + "tool_state": "{\"outWig\": {\"outWigType\": \"None\", \"__current_case__\": 0, \"outWigStrand\": \"false\"}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf-with-gtf\", \"__current_case__\": 1, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfile\": {\"__class__\": \"RuntimeValue\"}, \"sjdbGTFfeatureExon\": \"exon\", \"sjdbOverhang\": \"100\"}}, \"sc\": {\"solo_type\": \"CB_UMI_Simple\", \"__current_case__\": 0, \"input_types\": {\"use\": \"list_paired\", \"__current_case__\": 1, \"input_collection\": {\"__class__\": \"RuntimeValue\"}}, \"soloCBwhitelist\": {\"__class__\": \"RuntimeValue\"}, \"params\": {\"chemistry\": \"Cv3\", \"__current_case__\": 1}, \"soloBarcodeReadLength\": {\"__class__\": \"ConnectedValue\"}, \"umidedup\": {\"soloUMIdedup\": \"1MM_CR\", \"__current_case__\": 4, \"soloUMIfiltering\": \"-\"}, \"soloCBmatchWLtype\": \"1MM_multi\"}, \"solo\": {\"soloStrand\": \"Forward\", \"soloFeatures\": \"Gene\", \"wasp_conditional\": {\"waspOutputMode\": \"\", \"__current_case__\": 1}, \"filter\": {\"filter_type\": \"no_filter\", \"__current_case__\": 3, \"output_raw\": \"true\"}, \"soloOutFormatFeaturesGeneField3\": \"Gene Expression\", \"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\", \"GX\", \"GN\", \"CB\", \"UB\"], \"quantModeGene\": true, \"outSAMunmapped\": false, \"outSAMmapqUnique\": \"60\", \"junction_limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.7.11a+galaxy1", "type": "tool", "uuid": "cef740b0-fa95-4542-b08f-dbfca4bfb3e5", "when": null, @@ -294,7 +294,7 @@ }, "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "errors": null, "id": 6, "input_connections": { @@ -311,13 +311,13 @@ "label": "multiQC", "name": "MultiQC", "outputs": [ - { - "name": "stats", - "type": "input" - }, { "name": "html_report", "type": "html" + }, + { + "name": "stats", + "type": "tabular" } ], "position": { @@ -331,15 +331,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "abfd8a6544d7", + "changeset_revision": "f7e2f1eb3a16", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"genecounts\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.11+galaxy1", + "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"genecounts\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "a16bf20e-2bc9-45e7-a0a3-b5590212b973", "when": null, @@ -660,7 +660,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -705,7 +705,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -750,7 +750,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1001,8 +1001,8 @@ ] } }, - "tags": "", - "uuid": "415c1b14-3b63-4d27-8c34-42e452cb49f1" + "tags": [], + "uuid": "933626df-33e9-46ac-8206-d297a7fcb83a" }, "tool_id": null, "type": "subworkflow", @@ -1020,6 +1020,6 @@ "tags": [ "#single-cell" ], - "uuid": "19feac09-8db7-4e3f-9774-8b815918cfa7", + "uuid": "87f25ddb-a663-4582-9ec6-d0b4bef4109c", "version": 2 } \ No newline at end of file diff --git a/workflows/transcriptomics/brew3r/BREW3R.ga b/workflows/transcriptomics/brew3r/BREW3R.ga index 1c035db24..6f466b2c5 100644 --- a/workflows/transcriptomics/brew3r/BREW3R.ga +++ b/workflows/transcriptomics/brew3r/BREW3R.ga @@ -12,7 +12,7 @@ "format-version": "0.1", "license": "GPL-3.0-or-later", "name": "BREW3R", - "release": "0.1", + "release": "0.2", "report": { "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" }, @@ -389,7 +389,7 @@ }, "9": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy1", "errors": null, "id": 9, "input_connections": { @@ -428,15 +428,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy1", "tool_shed_repository": { - "changeset_revision": "3198f52bffaa", + "changeset_revision": "d3b0390f325f", "name": "brew3r_r", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"exclude_pattern\": \"\", \"filter_unstranded\": {\"__class__\": \"ConnectedValue\"}, \"gtf_to_extend\": {\"__class__\": \"ConnectedValue\"}, \"gtf_to_overlap\": {\"__class__\": \"ConnectedValue\"}, \"no_add\": false, \"sup_output\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.0.2+galaxy0", + "tool_version": "1.0.2+galaxy1", "type": "tool", "uuid": "c6a1e810-55f4-4c0e-9f19-d162503edbf0", "when": null, diff --git a/workflows/transcriptomics/brew3r/CHANGELOG.md b/workflows/transcriptomics/brew3r/CHANGELOG.md index 7a859c1bf..86b175116 100644 --- a/workflows/transcriptomics/brew3r/CHANGELOG.md +++ b/workflows/transcriptomics/brew3r/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [0.2] 2024-10-07 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy1` + ## [0.1] 2024-06-17 First release. diff --git a/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md b/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md index 80585c158..64d12ef64 100644 --- a/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md +++ b/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md @@ -1,5 +1,12 @@ # Changelog +## [0.9] 2024-09-23 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0` + ## [0.8] 2024-07-15 ### Automatic update diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 4b3b223bc..76be417ce 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -45,23 +45,11 @@ value: 89048730 delta: 8000000 'MultiQC on input dataset(s): Stats': - element_tests: - cutadapt: - asserts: - has_text: - text: "1057657 25033 25779 25250 1032407 78266618 3650637 73538382 6.041191149974054" - general_stats: - asserts: - has_text: - text: "GSM461177 82.8 854812.0" - sources: - asserts: - has_n_lines: - n: 4 - star: - asserts: - has_text_matching: - expression: "GSM461177 1032407.0 71.0 854812.0 82.8 70.65 10276[23].0 102412.0 1020[34][0-9].0 679.0 20.0 24.0 0.54 0.0 1.56 0.0 1.43 82072.0 7.95 32881.0 3.18 0.0 5.9 0.17 0 60888 1754" + asserts: + has_line: + line: "Sample STAR_mqc_generalstats_star_total_reads_1 STAR_mqc_generalstats_star_mapped_1 STAR_mqc_generalstats_star_mapped_percent_1 STAR_mqc_generalstats_star_uniquely_mapped_1 STAR_mqc_generalstats_star_uniquely_mapped_percent_1 STAR_mqc_generalstats_star_multimapped_1 Cutadapt_mqc_generalstats_cutadapt_percent_trimmed" + has_text_matching: + expression: "GSM461177\t1.0[0-9]*\t0.93[0-9]*\t90.[0-9]*\t0.8[0-9]*\t82.8[0-9]*\t0.08[0-9]*\t6.0[0-9]*" MultiQC webpage: asserts: - that: "has_text" diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index 22f14d9eb..ca98e047a 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -11,7 +11,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.8", + "release": "0.9", "name": "RNAseq_PE", "steps": { "0": { @@ -259,7 +259,7 @@ }, "9": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "errors": null, "id": 9, "input_connections": { @@ -315,15 +315,15 @@ "output_name": "report" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "aa784cb3810d", + "changeset_revision": "5eb7e84243f2", "name": "cutadapt", "owner": "lparsons", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"adapter_options\": {\"action\": \"trim\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"minimum_length2\": null, \"maximum_length\": null, \"maximum_length2\": null, \"max_n\": null, \"max_expected_errors\": null, \"max_average_error_rate\": null, \"discard_casava\": false, \"pair_filter\": \"any\"}, \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC\", \"adapter\": {\"__class__\": \"ConnectedValue\"}}, \"single_noindels\": false}], \"front_adapters\": [], \"anywhere_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Please use: For R2: - For Nextera: CTGTCTCTTATACACATCTGACGCTGCCGACGA - For TruSeq: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT\", \"adapter\": {\"__class__\": \"ConnectedValue\"}}, \"single_noindels\": false}], \"front_adapters2\": [], \"anywhere_adapters2\": []}, \"pair_adapters\": false}, \"other_trimming_options\": {\"cut\": \"0\", \"cut2\": \"0\", \"quality_cutoff\": \"30\", \"quality_cutoff2\": \"\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"poly_a\": false, \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"shorten_options_r2\": {\"shorten_values_r2\": \"False\", \"__current_case__\": 1}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"strip_suffix\": \"\", \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.9+galaxy0", + "tool_version": "4.9+galaxy1", "type": "tool", "uuid": "bb78142b-c185-40a6-b7c5-4fa9f6b3d314", "when": null, @@ -526,7 +526,7 @@ }, "14": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1", "errors": null, "id": 14, "input_connections": { @@ -616,15 +616,15 @@ "output_name": "splice_junctions" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1", "tool_shed_repository": { - "changeset_revision": "b0f2be869d6d", + "changeset_revision": "4014de1b6daf", "name": "rgrnastar", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"algo\": {\"params\": {\"settingsType\": \"full\", \"__current_case__\": 3, \"seed\": {\"seedSearchStartLmax\": \"50\", \"seedSearchStartLmaxOverLread\": \"1.0\", \"seedSearchLmax\": \"0\", \"seedMultimapNmax\": \"10000\", \"seedPerReadNmax\": \"1000\", \"seedPerWindowNmax\": \"50\", \"seedNoneLociPerWindow\": \"10\"}, \"align\": {\"alignIntronMin\": \"20\", \"alignIntronMax\": \"1000000\", \"alignMatesGapMax\": \"1000000\", \"alignSJoverhangMin\": \"8\", \"alignSJstitchMismatchNmax\": {\"alignSJstitchMismatchNmax1\": \"0\", \"alignSJstitchMismatchNmax2\": \"-1\", \"alignSJstitchMismatchNmax3\": \"0\", \"alignSJstitchMismatchNmax4\": \"0\"}, \"alignSJDBoverhangMin\": \"1\", \"alignSplicedMateMapLmin\": \"0\", \"alignSplicedMateMapLminOverLmate\": \"0.66\", \"alignWindowsPerReadNmax\": \"10000\", \"alignTranscriptsPerWindowNmax\": \"100\", \"alignTranscriptsPerReadNmax\": \"10000\", \"alignEndsType\": \"Local\", \"peOverlapNbasesMin\": \"0\", \"peOverlapMMp\": \"0.01\"}, \"chim_settings\": {\"chimSegmentMin\": \"12\", \"chimScoreMin\": \"0\", \"chimScoreDropMax\": \"20\", \"chimScoreSeparation\": \"10\", \"chimScoreJunctionNonGTAG\": \"-1\", \"chimJunctionOverhangMin\": \"20\", \"chimSegmentReadGapMax\": \"0\", \"chimFilter\": true, \"chimMainSegmentMultNmax\": \"10\", \"chimMultimapNmax\": \"1\", \"chimMultimapScoreRange\": \"1\"}, \"junction_limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}}, \"chimOutType\": \"\", \"filter\": {\"basic_filters\": [\"exclude_unmapped\"], \"output_params2\": {\"output_select2\": \"yes\", \"__current_case__\": 0, \"outFilterType\": true, \"outFilterMultimapScoreRange\": \"1\", \"outFilterMultimapNmax\": \"20\", \"outFilterMismatchNmax\": \"999\", \"outFilterMismatchNoverLmax\": \"0.3\", \"outFilterMismatchNoverReadLmax\": \"0.04\", \"outFilterScoreMin\": \"0\", \"outFilterScoreMinOverLread\": \"0.66\", \"outFilterMatchNmin\": \"0\", \"outFilterMatchNminOverLread\": \"0.66\", \"outSAMmultNmax\": \"-1\", \"outSAMtlen\": \"1\"}}, \"oformat\": {\"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\"], \"HI_offset\": \"1\", \"outSAMprimaryFlag\": \"OneBestScore\", \"outSAMmapqUnique\": \"255\"}, \"outWig\": {\"outWigType\": \"bedGraph\", \"__current_case__\": 1, \"outWigTypeSecondWord\": \"\", \"outWigStrand\": true, \"outWigReferencesPrefix\": \"-\", \"outWigNorm\": true}, \"perf\": {\"outBAMsortingBinsN\": \"50\", \"winAnchorMultimapNmax\": \"50\"}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf-with-gtf\", \"__current_case__\": 1, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfile\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfeatureExon\": \"exon\", \"sjdbOverhang\": \"100\", \"quantmode_output\": {\"quantMode\": \"GeneCounts\", \"__current_case__\": 1}}}, \"singlePaired\": {\"sPaired\": \"paired_collection\", \"__current_case__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"twopass\": {\"twopassMode\": \"None\", \"__current_case__\": 0, \"twopass_read_subset\": \"\", \"sj_precalculated\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.7.11a+galaxy0", + "tool_state": "{\"algo\": {\"params\": {\"settingsType\": \"full\", \"__current_case__\": 3, \"seed\": {\"seedSearchStartLmax\": \"50\", \"seedSearchStartLmaxOverLread\": \"1.0\", \"seedSearchLmax\": \"0\", \"seedMultimapNmax\": \"10000\", \"seedPerReadNmax\": \"1000\", \"seedPerWindowNmax\": \"50\", \"seedNoneLociPerWindow\": \"10\"}, \"align\": {\"alignIntronMin\": \"20\", \"alignIntronMax\": \"1000000\", \"alignMatesGapMax\": \"1000000\", \"alignSJoverhangMin\": \"8\", \"alignSJstitchMismatchNmax\": {\"alignSJstitchMismatchNmax1\": \"0\", \"alignSJstitchMismatchNmax2\": \"-1\", \"alignSJstitchMismatchNmax3\": \"0\", \"alignSJstitchMismatchNmax4\": \"0\"}, \"alignSJDBoverhangMin\": \"1\", \"alignSplicedMateMapLmin\": \"0\", \"alignSplicedMateMapLminOverLmate\": \"0.66\", \"alignWindowsPerReadNmax\": \"10000\", \"alignTranscriptsPerWindowNmax\": \"100\", \"alignTranscriptsPerReadNmax\": \"10000\", \"alignEndsType\": \"Local\", \"peOverlapNbasesMin\": \"0\", \"peOverlapMMp\": \"0.01\"}, \"chim_settings\": {\"chimSegmentMin\": \"12\", \"chimScoreMin\": \"0\", \"chimScoreDropMax\": \"20\", \"chimScoreSeparation\": \"10\", \"chimScoreJunctionNonGTAG\": \"-1\", \"chimJunctionOverhangMin\": \"20\", \"chimSegmentReadGapMax\": \"0\", \"chimFilter\": true, \"chimMainSegmentMultNmax\": \"10\", \"chimMultimapNmax\": \"1\", \"chimMultimapScoreRange\": \"1\"}, \"junction_limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}}, \"chimOutType\": \"\", \"filter\": {\"basic_filters\": [\"exclude_unmapped\"], \"output_params2\": {\"output_select2\": \"yes\", \"__current_case__\": 0, \"outFilterType\": true, \"outFilterMultimapScoreRange\": \"1\", \"outFilterMultimapNmax\": \"20\", \"outFilterMismatchNmax\": \"999\", \"outFilterMismatchNoverLmax\": \"0.3\", \"outFilterMismatchNoverReadLmax\": \"0.04\", \"outFilterScoreMin\": \"0\", \"outFilterScoreMinOverLread\": \"0.66\", \"outFilterMatchNmin\": \"0\", \"outFilterMatchNminOverLread\": \"0.66\", \"outSAMmultNmax\": \"-1\", \"outSAMtlen\": \"1\"}}, \"oformat\": {\"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\"], \"HI_offset\": \"1\", \"outSAMprimaryFlag\": \"OneBestScore\", \"outSAMmapqUnique\": \"255\", \"wasp_conditional\": {\"waspOutputMode\": \"\", \"__current_case__\": 1}}, \"outWig\": {\"outWigType\": \"bedGraph\", \"__current_case__\": 1, \"outWigTypeSecondWord\": \"\", \"outWigStrand\": true, \"outWigReferencesPrefix\": \"-\", \"outWigNorm\": true}, \"perf\": {\"outBAMsortingBinsN\": \"50\", \"winAnchorMultimapNmax\": \"50\"}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf-with-gtf\", \"__current_case__\": 1, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfile\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfeatureExon\": \"exon\", \"sjdbOverhang\": \"100\", \"quantmode_output\": {\"quantMode\": \"GeneCounts\", \"__current_case__\": 1}}}, \"singlePaired\": {\"sPaired\": \"paired_collection\", \"__current_case__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"twopass\": {\"twopassMode\": \"None\", \"__current_case__\": 0, \"twopass_read_subset\": \"\", \"sj_precalculated\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.7.11a+galaxy1", "type": "tool", "uuid": "8f30d1b2-6458-491b-bf46-9bdcca9db085", "when": null, @@ -648,7 +648,7 @@ }, "15": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "errors": null, "id": 15, "input_connections": { @@ -669,10 +669,6 @@ "label": "MultiQC", "name": "MultiQC", "outputs": [ - { - "name": "stats", - "type": "input" - }, { "name": "plots", "type": "input" @@ -680,6 +676,10 @@ { "name": "html_report", "type": "html" + }, + { + "name": "stats", + "type": "tabular" } ], "position": { @@ -693,15 +693,15 @@ "output_name": "plots" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "abfd8a6544d7", + "changeset_revision": "f7e2f1eb3a16", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"genecounts\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.11+galaxy1", + "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"genecounts\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "da516e4c-e074-4930-a6f8-a68d9844d386", "when": null, @@ -897,7 +897,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1055,7 +1055,7 @@ } }, "tags": [], - "uuid": "c548dfba-fd18-4f89-bba4-722f9a1cc300" + "uuid": "fdfcabc8-5014-4574-85ab-0182cb11750f" }, "tool_id": null, "type": "subworkflow", @@ -1385,7 +1385,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1434,7 +1434,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1634,7 +1634,7 @@ } }, "tags": [], - "uuid": "3d850804-e1e9-4517-8f33-ecba0c527b73" + "uuid": "879fffe0-897e-44c2-af76-934f0a79534c" }, "tool_id": null, "type": "subworkflow", @@ -1802,7 +1802,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" diff --git a/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md b/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md index d87e3c0e8..389e9e12d 100644 --- a/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md +++ b/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md @@ -1,5 +1,12 @@ # Changelog +## [0.9] 2024-09-23 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0` + ## [0.8] 2024-07-15 ### Automatic update diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml index 2c0d813b7..6be85c478 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml @@ -34,24 +34,12 @@ has_size: value: 43037033 delta: 4000000 - 'MultiQC on input dataset(s): Stats': - element_tests: - cutadapt: - asserts: - has_text: - text: "\t1057657\t25033\t6191\t1051466\t39133309\t1439589\t37547108\t4.053327051898423" - general_stats: - asserts: - has_text: - text: "GSM461177\t82.86\t871202.0\t4.053327051898423" - sources: - asserts: - has_n_lines: - n: 4 - star: - asserts: - has_text_matching: - expression: "GSM461177\t1051466.0\t35.0\t871202.0\t82.86\t35.4\t51184.0\t50995.0\t50810.0\t343.0\t12.0\t19.0\t0.48\t0.0\t1.48\t0.0\t1.36\t9180[89].0\t8.73\t34515.0\t3.28\t0.0\t4.76\t0.37\t0\t5005[01]\t3890" + 'MultiQC on input dataset(s): Stats': + asserts: + has_line: + line: "Sample STAR_mqc_generalstats_star_total_reads_1 STAR_mqc_generalstats_star_mapped_1 STAR_mqc_generalstats_star_mapped_percent_1 STAR_mqc_generalstats_star_uniquely_mapped_1 STAR_mqc_generalstats_star_uniquely_mapped_percent_1 STAR_mqc_generalstats_star_multimapped_1 Cutadapt_mqc_generalstats_cutadapt_percent_trimmed" + has_text_matching: + expression: "GSM461177\t1.0[0-9]*\t0.96[0-9]*\t91.[0-9]*\t0.8[0-9]*\t82.8[0-9]*\t0.091[0-9]*\t4.0[0-9]*" MultiQC webpage: asserts: - that: "has_text" diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga index b18022f50..509d68a0d 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga @@ -12,7 +12,7 @@ "format-version": "0.1", "license": "MIT", "name": "RNAseq_SR", - "release": "0.8", + "release": "0.9", "steps": { "0": { "annotation": "Should be a list of single-read RNA-seq fastqs", @@ -232,7 +232,7 @@ }, "8": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "errors": null, "id": 8, "input_connections": { @@ -284,15 +284,15 @@ "output_name": "report" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "aa784cb3810d", + "changeset_revision": "5eb7e84243f2", "name": "cutadapt", "owner": "lparsons", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adapter_options\": {\"action\": \"trim\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"minimum_length2\": null, \"maximum_length\": null, \"maximum_length2\": null, \"max_n\": null, \"max_expected_errors\": null, \"max_average_error_rate\": null, \"discard_casava\": false, \"pair_filter\": \"any\"}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC\", \"adapter\": {\"__class__\": \"ConnectedValue\"}}, \"single_noindels\": false}], \"front_adapters\": [], \"anywhere_adapters\": []}}, \"other_trimming_options\": {\"cut\": \"0\", \"cut2\": \"0\", \"quality_cutoff\": \"30\", \"quality_cutoff2\": \"\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"poly_a\": false, \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"shorten_options_r2\": {\"shorten_values_r2\": \"False\", \"__current_case__\": 1}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"strip_suffix\": \"\", \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.9+galaxy0", + "tool_version": "4.9+galaxy1", "type": "tool", "uuid": "4d39b70d-c852-4c42-9e0d-f3641d632543", "when": null, @@ -495,7 +495,7 @@ }, "13": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1", "errors": null, "id": 13, "input_connections": { @@ -585,15 +585,15 @@ "output_name": "splice_junctions" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1", "tool_shed_repository": { - "changeset_revision": "b0f2be869d6d", + "changeset_revision": "4014de1b6daf", "name": "rgrnastar", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"algo\": {\"params\": {\"settingsType\": \"full\", \"__current_case__\": 3, \"seed\": {\"seedSearchStartLmax\": \"50\", \"seedSearchStartLmaxOverLread\": \"1.0\", \"seedSearchLmax\": \"0\", \"seedMultimapNmax\": \"10000\", \"seedPerReadNmax\": \"1000\", \"seedPerWindowNmax\": \"50\", \"seedNoneLociPerWindow\": \"10\"}, \"align\": {\"alignIntronMin\": \"20\", \"alignIntronMax\": \"1000000\", \"alignMatesGapMax\": \"1000000\", \"alignSJoverhangMin\": \"8\", \"alignSJstitchMismatchNmax\": {\"alignSJstitchMismatchNmax1\": \"0\", \"alignSJstitchMismatchNmax2\": \"-1\", \"alignSJstitchMismatchNmax3\": \"0\", \"alignSJstitchMismatchNmax4\": \"0\"}, \"alignSJDBoverhangMin\": \"1\", \"alignSplicedMateMapLmin\": \"0\", \"alignSplicedMateMapLminOverLmate\": \"0.66\", \"alignWindowsPerReadNmax\": \"10000\", \"alignTranscriptsPerWindowNmax\": \"100\", \"alignTranscriptsPerReadNmax\": \"10000\", \"alignEndsType\": \"Local\", \"peOverlapNbasesMin\": \"0\", \"peOverlapMMp\": \"0.01\"}, \"chim_settings\": {\"chimSegmentMin\": \"12\", \"chimScoreMin\": \"0\", \"chimScoreDropMax\": \"20\", \"chimScoreSeparation\": \"10\", \"chimScoreJunctionNonGTAG\": \"-1\", \"chimJunctionOverhangMin\": \"20\", \"chimSegmentReadGapMax\": \"0\", \"chimFilter\": true, \"chimMainSegmentMultNmax\": \"10\", \"chimMultimapNmax\": \"1\", \"chimMultimapScoreRange\": \"1\"}, \"junction_limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}}, \"chimOutType\": \"\", \"filter\": {\"basic_filters\": [\"exclude_unmapped\"], \"output_params2\": {\"output_select2\": \"yes\", \"__current_case__\": 0, \"outFilterType\": true, \"outFilterMultimapScoreRange\": \"1\", \"outFilterMultimapNmax\": \"20\", \"outFilterMismatchNmax\": \"999\", \"outFilterMismatchNoverLmax\": \"0.3\", \"outFilterMismatchNoverReadLmax\": \"0.04\", \"outFilterScoreMin\": \"0\", \"outFilterScoreMinOverLread\": \"0.66\", \"outFilterMatchNmin\": \"0\", \"outFilterMatchNminOverLread\": \"0.66\", \"outSAMmultNmax\": \"-1\", \"outSAMtlen\": \"1\"}}, \"oformat\": {\"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\"], \"HI_offset\": \"1\", \"outSAMprimaryFlag\": \"OneBestScore\", \"outSAMmapqUnique\": \"255\"}, \"outWig\": {\"outWigType\": \"bedGraph\", \"__current_case__\": 1, \"outWigTypeSecondWord\": \"\", \"outWigStrand\": true, \"outWigReferencesPrefix\": \"-\", \"outWigNorm\": true}, \"perf\": {\"outBAMsortingBinsN\": \"50\", \"winAnchorMultimapNmax\": \"50\"}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf-with-gtf\", \"__current_case__\": 1, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfile\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfeatureExon\": \"exon\", \"sjdbOverhang\": \"100\", \"quantmode_output\": {\"quantMode\": \"GeneCounts\", \"__current_case__\": 1}}}, \"singlePaired\": {\"sPaired\": \"single\", \"__current_case__\": 0, \"input1\": {\"__class__\": \"ConnectedValue\"}}, \"twopass\": {\"twopassMode\": \"None\", \"__current_case__\": 0, \"twopass_read_subset\": \"\", \"sj_precalculated\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - 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"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "errors": null, "id": 14, "input_connections": { @@ -638,10 +638,6 @@ "label": "MultiQC", "name": "MultiQC", "outputs": [ - { - "name": "stats", - "type": "input" - }, { "name": "plots", "type": "input" @@ -649,6 +645,10 @@ { "name": "html_report", "type": "html" + }, + { + "name": "stats", + "type": "tabular" } ], "position": { @@ -662,15 +662,15 @@ "output_name": "plots" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "abfd8a6544d7", + "changeset_revision": "f7e2f1eb3a16", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"genecounts\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.11+galaxy1", + "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"genecounts\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "ba4d9ac2-f8b6-43bc-bc5f-e542c44441cd", "when": null, @@ -866,7 +866,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1024,7 +1024,7 @@ } }, "tags": [], - "uuid": "0af80b84-9ced-41d5-8315-40dfe8c1b638" + "uuid": "d629f889-14c9-4a3f-bf9f-1b31117e3191" }, "tool_id": null, "type": "subworkflow", @@ -1354,7 +1354,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1403,7 +1403,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1603,7 +1603,7 @@ } }, "tags": [], - "uuid": "7bf438af-cb14-4fd2-ba15-2e86b44ed0cb" + "uuid": "f97bb6df-6f4c-4ccd-8108-6b2d88f35ff4" }, "tool_id": null, "type": "subworkflow", @@ -1771,7 +1771,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu"