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 8b77724e8..067e0e5ba 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 @@ -59,19 +59,19 @@ Assembly statistics for Hap1 and Hap2: asserts: has_line: - line: "# contigs 85 23" + line: "# contigs 81 27" usable hap1 gfa: asserts: has_n_lines: - n: 175 + n: 167 Hifiasm Trio hap1: asserts: has_n_lines: - n: 170 + n: 162 Busco Summary Hap1: asserts: has_text: - text: "C:1.2%[S:1.2%,D:0.0%],F:0.4%,M:98.4%,n:3354" + text: "C:1.2%[S:1.1%,D:0.0%],F:0.4%,M:98.4%" Nx Plot: asserts: has_size: 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 d9b21ec9f..90391a239 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 @@ -15,7 +15,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.2", + "release": "0.3", "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" @@ -199,8 +199,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 14.278967454027603, - "top": 893.0522085856591 + "left": 33.17695496536256, + "top": 890.2068997739406 }, "tool_id": null, "tool_state": "{\"default\": 37, \"parameter_type\": \"integer\", \"optional\": true}", @@ -208,13 +208,7 @@ "type": "parameter_input", "uuid": "a5987ed3-6fdb-49c7-92d0-5b2f78a9bbb9", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "1bb5df96-d731-4e12-b902-ec6e1d723b07" - } - ] + "workflow_outputs": [] }, "7": { "annotation": "", @@ -241,13 +235,7 @@ "type": "parameter_input", "uuid": "ca553be3-e5c9-4770-bd61-d50ed05c69ae", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "9829d67c-d793-44c9-9b53-9c3ebd2155a8" - } - ] + "workflow_outputs": [] }, "8": { "annotation": "Taxonomic lineage for the organism being assembled for Busco analysis", @@ -274,13 +262,7 @@ "type": "parameter_input", "uuid": "9762d451-eb6f-4f0c-8203-7094f46ea771", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "9dff2868-bf8a-4443-87c9-52f5b8975bdb" - } - ] + "workflow_outputs": [] }, "9": { "annotation": "If empty, read coverage will be estimated from the Genomescope parameters. ", @@ -307,13 +289,7 @@ "type": "parameter_input", "uuid": "ffcf874f-594d-4d58-99dc-73ef566bcc88", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "28a260f0-a63e-4743-ba41-6544e4f423a9" - } - ] + "workflow_outputs": [] }, "10": { "annotation": "GenomeScope model parameters generated by K-mer profiling workflow", @@ -394,13 +370,7 @@ "type": "parameter_input", "uuid": "eb8c0bcc-14c8-4b3d-b73f-442eae454b82", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "b178a102-00b1-45ae-8404-2c7c544cdeee" - } - ] + "workflow_outputs": [] }, "13": { "annotation": "", @@ -427,13 +397,7 @@ "type": "data_input", "uuid": "80ff22ac-1a58-4f89-bf52-48f18d8f71f9", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "c2cf45d3-af1d-49d6-9d77-41065f57fcdb" - } - ] + "workflow_outputs": [] }, "14": { "annotation": "", @@ -460,13 +424,7 @@ "type": "parameter_input", "uuid": "c5651e7e-31d4-41b7-a590-e2fadc7f59e9", "when": null, - 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"21": { + "23": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "errors": null, - "id": 21, + "id": 23, "input_connections": { "infile": { - "id": 18, + "id": 19, "output_name": "output" } }, @@ -790,7 +820,7 @@ }, "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" @@ -802,14 +832,14 @@ "when": null, "workflow_outputs": [] }, - "22": { + "24": { "annotation": "", "content_id": "param_value_from_file", "errors": null, - "id": 22, + "id": 24, "input_connections": { "input1": { - "id": 20, + "id": 22, "output_name": "out_file1" } }, @@ -841,14 +871,14 @@ "when": null, "workflow_outputs": [] }, - "23": { + "25": { "annotation": "", "content_id": "Convert characters1", "errors": null, - "id": 23, + "id": 25, "input_connections": { "input": { - "id": 21, + "id": 23, "output_name": "outfile" } }, @@ -880,18 +910,18 @@ "when": null, "workflow_outputs": [] }, - "24": { + "26": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, - "id": 24, + "id": 26, "input_connections": { "style_cond|type_cond|pick_from_0|value": { "id": 9, "output_name": "output" }, "style_cond|type_cond|pick_from_1|value": { - "id": 22, + "id": 24, "output_name": "integer_param" } }, @@ -931,14 +961,14 @@ "when": null, "workflow_outputs": [] }, - "25": { + "27": { "annotation": "", "content_id": "Cut1", "errors": null, - "id": 25, + "id": 27, "input_connections": { "input": { - "id": 23, + "id": 25, "output_name": "out_file1" } }, @@ -970,27 +1000,27 @@ "when": null, "workflow_outputs": [] }, - "26": { + "28": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.20.0+galaxy0", "errors": null, - "id": 26, + "id": 28, "input_connections": { "assembly_options|hom_cov": { - "id": 24, + "id": 26, "output_name": "integer_param" }, "filter_bits": { - "id": 6, - "output_name": "output" + "id": 17, + "output_name": "integer_param" }, "mode|reads": { "id": 16, "output_name": "out1" }, "mode|trio_dual": { - "id": 12, - "output_name": "output" + "id": 20, + "output_name": "boolean_param" }, "mode|trioinput|hap1_reads": { "id": 1, @@ -1078,28 +1108,28 @@ "output_name": "raw_unitigs_trio" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.20.0+galaxy0", "tool_shed_repository": { - "changeset_revision": "284a1cb82b61", + "changeset_revision": "5161f204ba63", "name": "hifiasm", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"advanced_options\": {\"advanced_selector\": \"blank\", \"__current_case__\": 0}, \"assembly_options\": {\"assembly_selector\": \"set\", \"__current_case__\": 1, \"cleaning_rounds\": \"4\", \"adapter_length\": \"0\", \"pop_contigs\": \"10000000\", \"pop_unitigs\": \"100000\", \"remove_tips\": \"3\", \"max_overlap\": \"0.8\", \"min_overlap\": \"0.2\", \"disable_post_join\": false, \"ignore_error_corrected\": false, \"hom_cov\": {\"__class__\": \"ConnectedValue\"}}, \"bins_out\": false, \"filter_bits\": {\"__class__\": \"ConnectedValue\"}, \"hic_partition\": {\"hic_partition_selector\": \"blank\", \"__current_case__\": 0}, \"log_out\": true, \"mode\": {\"mode_selector\": \"trio\", \"__current_case__\": 1, \"reads\": {\"__class__\": \"ConnectedValue\"}, \"trioinput\": {\"trio_input_selector\": \"reads\", \"__current_case__\": 0, \"hap1_reads\": {\"__class__\": \"ConnectedValue\"}, \"hap2_reads\": {\"__class__\": \"ConnectedValue\"}}, \"max_kmers\": \"2\", \"min_kmers\": \"5\", \"yak_kmer_length\": \"31\", \"trio_dual\": {\"__class__\": \"ConnectedValue\"}}, \"ont_integration\": {\"ont_integration_selector\": \"blank\", \"__current_case__\": 0}, \"purge_options\": {\"purge_selector\": \"blank\", \"__current_case__\": 0}, \"scaffolding_options\": {\"scaffold_selector\": \"blank\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - 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"id": 51, + "id": 53, "input_connections": { "input1": { - "id": 43, + "id": 45, "output_name": "outfile" }, "input2": { - "id": 42, + "id": 44, "output_name": "outfile" } }, @@ -3783,14 +3803,14 @@ "when": null, "workflow_outputs": [] }, - "52": { + "54": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2", "errors": null, - "id": 52, + "id": 54, "input_connections": { "input": { - "id": 51, + "id": 53, "output_name": "out_file1" } }, @@ -3823,15 +3843,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"complement\": \"--complement\", \"cut_type_options\": {\"cut_element\": \"-f\", \"__current_case__\": 0, \"delimiter\": \"\", \"colnames_option\": {\"header\": \"N\", \"__current_case__\": 1, \"list\": [\"3\"]}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.3+galaxy1", + "tool_version": "9.3+galaxy2", "type": "tool", "uuid": "b6796224-1789-45fd-8392-3237462c9071", "when": null, @@ -3843,14 +3863,14 @@ } ] }, - "53": { + "55": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "errors": null, - "id": 53, + "id": 55, "input_connections": { "infile": { - "id": 52, + "id": 54, "output_name": "output" } }, @@ -3876,7 +3896,7 @@ }, "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" @@ -3899,6 +3919,6 @@ "VGP", "Reviewed" ], - "uuid": "3cacf798-0f32-43b9-82c0-2d8f76312c80", - "version": 8 -} \ No newline at end of file + "uuid": "bd09a130-801c-4cb8-b848-ab90b3161322", + "version": 3 +} 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 084dab9b6..bdeb6cb38 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 +1,15 @@ # Changelog +## [0.3] 2024-11-11 + +### 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/iuc/multiqc/multiqc/1.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.20.0+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2` + ## [0.2] 2024-08-12 ### Added