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 5bd6abc7c..2a015378e 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 @@ -19,7 +19,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.1", + "release": "0.1.2", "name": "Assembly-Hifi-HiC-phasing-VGP4", "steps": { "0": { @@ -39,7 +39,7 @@ "outputs": [], "position": { "left": 0, - "top": 601.6407359730115 + "top": 600.0407323343393 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", @@ -65,8 +65,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 360.5990149758079, - "top": 821.284901012074 + "left": 52.58746337890625, + "top": 729.2749963613278 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", @@ -92,8 +92,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 627.265722101385, - "top": 928.5504890210702 + "left": 127.26248168945312, + "top": 858.1499353261715 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -119,11 +119,11 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 368.9063158902255, - "top": 1208.8194876006157 + "left": 240.10000610351562, + "top": 1024.0124841542965 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": \"\"}", + "tool_state": "{\"optional\": false, \"tag\": \"genomescope_params\"}", "tool_version": null, "type": "data_input", "uuid": "0735f7ce-74e8-4ae0-8142-e6d2fd89c89e", @@ -146,11 +146,11 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 377.2136225844875, - "top": 1460.503688003078 + "left": 305.2124938964844, + "top": 1224.7852478027344 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": \"\"}", + "tool_state": "{\"optional\": false, \"tag\": \"genomescope_summ\"}", "tool_version": null, "type": "data_input", "uuid": "1844cbb3-ba5f-4997-a3cd-ce70f4570a99", @@ -173,11 +173,11 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 1730.5817343971949, - "top": 419.62677926728225 + "left": 338.18748705505163, + "top": 1393.2250061035156 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": \"\"}", + "tool_state": "{\"optional\": false, \"tag\": \"meryl_db\"}", "tool_version": null, "type": "data_input", "uuid": "fcb0f86e-455a-4a6e-9c86-d8994caf0493", @@ -185,68 +185,68 @@ "workflow_outputs": [] }, "6": { - "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.", + "annotation": "", "content_id": null, "errors": null, "id": 6, "input_connections": {}, "inputs": [ { - "description": "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.", - "name": "Bits for bloom filter" + "description": "", + "name": "SAK input file" } ], - "label": "Bits for bloom filter", - "name": "Input parameter", + "label": "SAK input file", + "name": "Input dataset", "outputs": [], "position": { - "left": 906.03125, - "top": 1704.0625 + "left": 358.20002636559843, + "top": 1550.8499755859375 }, "tool_id": null, - "tool_state": "{\"default\": 37, \"parameter_type\": \"integer\", \"optional\": true}", + "tool_state": "{\"optional\": true, \"tag\": \"\"}", "tool_version": null, - "type": "parameter_input", - "uuid": "b949921b-95a3-4d43-81b2-4006a4909e4b", + "type": "data_input", + "uuid": "557a2e2b-008c-4566-836a-6509950aa85b", "when": null, "workflow_outputs": [ { "label": null, "output_name": "output", - "uuid": "105bb189-a2d4-4cfc-8cb8-39ab70af0277" + "uuid": "19782069-2309-495f-a249-75893193f27a" } ] }, "7": { - "annotation": "", + "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": 7, "input_connections": {}, "inputs": [ { - "description": "", - "name": "SAK input file" + "description": "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.", + "name": "Bits for bloom filter" } ], - "label": "SAK input file", - "name": "Input dataset", + "label": "Bits for bloom filter", + "name": "Input parameter", "outputs": [], "position": { - "left": 1785.3040059407554, - "top": 1450.859578450521 + "left": 906.03125, + "top": 1702.4624963613278 }, "tool_id": null, - "tool_state": "{\"optional\": true, \"tag\": \"\"}", + "tool_state": "{\"default\": 37, \"parameter_type\": \"integer\", \"optional\": true}", "tool_version": null, - "type": "data_input", - "uuid": "557a2e2b-008c-4566-836a-6509950aa85b", + "type": "parameter_input", + "uuid": "b949921b-95a3-4d43-81b2-4006a4909e4b", "when": null, "workflow_outputs": [ { "label": null, "output_name": "output", - "uuid": "2a6cc6ed-3248-4048-9208-a683e43f1c0f" + "uuid": "de7c94f5-9275-4ec4-91f1-2ac4f486ab75" } ] }, @@ -267,7 +267,7 @@ "outputs": [], "position": { "left": 3629.8615195534453, - "top": 1523.559107924953 + "top": 1521.9591042862808 }, "tool_id": null, "tool_state": "{\"default\": \"Hap1\", \"parameter_type\": \"text\", \"optional\": true}", @@ -279,7 +279,7 @@ { "label": null, "output_name": "output", - "uuid": "2eef5014-6358-446d-9d97-4a9b43f83e75" + "uuid": "423f5dec-facb-45ab-a662-f07d53103ae9" } ] }, @@ -300,7 +300,7 @@ "outputs": [], "position": { "left": 3641.8580719918923, - "top": 1674.3751294685135 + "top": 1672.7751258298413 }, "tool_id": null, "tool_state": "{\"default\": \"Hap2\", \"parameter_type\": \"text\", \"optional\": true}", @@ -312,7 +312,7 @@ { "label": null, "output_name": "output", - "uuid": "5f6be88c-dc8a-40ce-8865-c36f26d826d7" + "uuid": "d85aabed-d996-4a80-bb8b-cbbf191a3e0a" } ] }, @@ -342,7 +342,7 @@ ], "position": { "left": 476.8230091441762, - "top": 589.340302438447 + "top": 587.7402987997748 }, "post_job_actions": { "HideDatasetActionreport": { @@ -407,7 +407,7 @@ ], "position": { "left": 623.1337807395242, - "top": 1208.8194876006157 + "top": 1207.2194839619435 }, "post_job_actions": { "HideDatasetActionout_file1": { @@ -452,7 +452,7 @@ ], "position": { "left": 616.7448795203007, - "top": 1458.837058327415 + "top": 1457.2370546887428 }, "post_job_actions": { "HideDatasetActionoutput": { @@ -501,7 +501,7 @@ ], "position": { "left": 1017.3959674257222, - "top": 787.7344304865057 + "top": 786.1344268478335 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", @@ -540,7 +540,7 @@ ], "position": { "left": 875.2518393776635, - "top": 1212.2222900390627 + "top": 1210.6222864003905 }, "post_job_actions": { "HideDatasetActionout_file1": { @@ -579,7 +579,7 @@ ], "position": { "left": 872.2483548251066, - "top": 1459.5748438979645 + "top": 1457.9748402592923 }, "post_job_actions": { "HideDatasetActionoutfile": { @@ -624,7 +624,7 @@ ], "position": { "left": 1109.154712670362, - "top": 1218.6660569445944 + "top": 1217.0660533059222 }, "post_job_actions": { "RenameDatasetActioninteger_param": { @@ -665,7 +665,7 @@ ], "position": { "left": 1116.4237051299124, - "top": 1467.821248372396 + "top": 1466.2212447337238 }, "post_job_actions": { "HideDatasetActionout_file1": { @@ -693,7 +693,7 @@ "output_name": "integer_param" }, "filter_bits": { - "id": 6, + "id": 7, "output_name": "output" }, "hic_partition|h1": { @@ -744,7 +744,7 @@ ], "position": { "left": 1650.198023834119, - "top": 729.0981977671058 + "top": 727.4981941284336 }, "post_job_actions": { "HideDatasetActionhic_acontig_graph": { @@ -829,7 +829,7 @@ ], "position": { "left": 1364.3925291119203, - "top": 1599.019091057055 + "top": 1597.4190874183828 }, "post_job_actions": { "HideDatasetActionout_file1": { @@ -873,7 +873,7 @@ ], "position": { "left": 2078.7762035023084, - "top": 3.9236357717803685 + "top": 2.3236321331081626 }, "post_job_actions": { "RenameDatasetActionoutput": { @@ -922,7 +922,7 @@ "output_name": "hic_balanced_contig_hap1_graph" }, "mode_condition|swiss_army_knife": { - "id": 7, + "id": 6, "output_name": "output" } }, @@ -937,7 +937,7 @@ ], "position": { "left": 2233.6199904933123, - "top": 369.32299064867425 + "top": 367.72298701000204 }, "post_job_actions": { "HideDatasetActionoutput": { @@ -971,7 +971,7 @@ "output_name": "hic_balanced_contig_hap2_graph" }, "mode_condition|swiss_army_knife": { - "id": 7, + "id": 6, "output_name": "output" } }, @@ -986,7 +986,7 @@ ], "position": { "left": 2240.694704922763, - "top": 636.0591079249527 + "top": 634.4591042862805 }, "post_job_actions": { "HideDatasetActionoutput": { @@ -1035,7 +1035,7 @@ } ], "position": { - "left": 2414.062661835642, + "left": 2480.4624938964844, "top": 0 }, "post_job_actions": { @@ -1096,7 +1096,7 @@ ], "position": { "left": 2310.4689858176494, - "top": 961.6668701171877 + "top": 960.0668664785155 }, "post_job_actions": { "TagDatasetActionoutfile": { @@ -1143,7 +1143,7 @@ ], "position": { "left": 2835.987005198547, - "top": 1467.2530248543883 + "top": 1465.653021215716 }, "post_job_actions": { "RenameDatasetActionstats": { @@ -1197,7 +1197,7 @@ ], "position": { "left": 2836.927541097006, - "top": 1803.8369843454075 + "top": 1802.2369807067353 }, "post_job_actions": { "RenameDatasetActionstats": { @@ -1251,7 +1251,7 @@ ], "position": { "left": 1645.6251433401399, - "top": 1621.8578916607485 + "top": 1620.2578880220763 }, "post_job_actions": { "RenameDatasetActioninteger_param": { @@ -1304,8 +1304,8 @@ } ], "position": { - "left": 2487.5695199677443, - "top": 342.17880711411 + "left": 2490.762481689453, + "top": 332.57501220703125 }, "post_job_actions": { "RenameDatasetActionoutput": { @@ -1365,7 +1365,7 @@ ], "position": { "left": 2490.9810152920813, - "top": 512.5868363813922 + "top": 510.98683274272 }, "post_job_actions": { "RenameDatasetActionoutput": { @@ -1419,7 +1419,7 @@ "outputs": [], "position": { "left": 3927.4223327636723, - "top": 833.7675152402937 + "top": 832.1675116016215 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -1794,7 +1794,7 @@ "outputs": [], "position": { "left": 3922.431136622574, - "top": 1057.8214703184187 + "top": 1056.2214666797465 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -2179,7 +2179,7 @@ ], "position": { "left": 2827.101065895775, - "top": 1285.946470318419 + "top": 1284.3464666797468 }, "post_job_actions": { "RenameDatasetActionstats": { @@ -2237,7 +2237,7 @@ ], "position": { "left": 2835.8424100008883, - "top": 1631.1285770300665 + "top": 1629.5285733913943 }, "post_job_actions": { "RenameDatasetActionstats": { @@ -2303,7 +2303,7 @@ ], "position": { "left": 3074.6484375, - "top": 65.95703125 + "top": 64.3570276113278 }, "post_job_actions": { "TagDatasetActionbusco_missing": { @@ -2348,15 +2348,15 @@ "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 Summary Image Hap1", + "output_name": "summary_image", + "uuid": "cfac3083-4c1e-4bb4-91a5-eba5d19f2757" } ] }, @@ -2402,7 +2402,7 @@ ], "position": { "left": 2855.921875, - "top": 789.0859375 + "top": 787.4859338613278 }, "post_job_actions": { "HideDatasetActionlog_file": { @@ -2507,7 +2507,7 @@ ], "position": { "left": 3079.7265625, - "top": 499.28515625 + "top": 497.6851526113278 }, "post_job_actions": { "TagDatasetActionbusco_missing": { @@ -2552,15 +2552,15 @@ "uuid": "08066bc3-0992-4606-844d-16be3c56691a", "when": null, "workflow_outputs": [ - { - "label": "Busco Summary Hap2", - "output_name": "busco_sum", - "uuid": "bf7e959c-5252-467e-bb58-2b8cabbd0f3b" - }, { "label": "Busco Summary Image Hap2", "output_name": "summary_image", "uuid": "84725fc4-3480-44a2-abc0-abc8f54addb1" + }, + { + "label": "Busco Summary Hap2", + "output_name": "busco_sum", + "uuid": "bf7e959c-5252-467e-bb58-2b8cabbd0f3b" } ] }, @@ -2595,7 +2595,7 @@ "outputs": [], "position": { "left": 4346.40625, - "top": 866.4609375 + "top": 864.8609338613278 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -3108,16 +3108,6 @@ "label": "Size Plot", "output_name": "Size Plot", "uuid": "03a0d2a8-c2d5-4ca7-80fe-7d04d1c4894a" - }, - { - "label": null, - "output_name": "2:output", - "uuid": "8614c252-637a-48dc-a751-9a3fea85b376" - }, - { - "label": null, - "output_name": "3:output", - "uuid": "b1b37b5e-092a-4bcb-87ab-f8b74abe1ebb" } ] }, @@ -3143,7 +3133,7 @@ ], "position": { "left": 3176.285044352214, - "top": 1140.6685569069605 + "top": 1139.0685532682883 }, "post_job_actions": { "HideDatasetActionoutfile": { @@ -3188,7 +3178,7 @@ ], "position": { "left": 3177.439533580434, - "top": 1537.5955292672825 + "top": 1535.9955256286103 }, "post_job_actions": { "HideDatasetActionoutfile": { @@ -3233,7 +3223,7 @@ ], "position": { "left": 3407.691331343218, - "top": 1368.6198841441765 + "top": 1367.0198805055043 }, "post_job_actions": { "HideDatasetActionout_file1": { @@ -3276,7 +3266,7 @@ ], "position": { "left": 3649.617149584222, - "top": 1140.9336085464017 + "top": 1139.3336049077295 }, "post_job_actions": { "TagDatasetActionout_file1": { @@ -3306,6 +3296,6 @@ "VGP", "Reviewed" ], - "uuid": "e6c42d60-3c0c-4c40-890a-0f5db9962b30", - "version": 17 + "uuid": "634604bc-4a32-4c35-9953-81b4f44751d9", + "version": 4 } \ 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 92bf39f8e..f4739c246 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 @@ -7,6 +7,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unreleased] +## [0.1.2] - 2023-11-07 + +- Added input filtering based on tags. Rearranged input ordering. + ## [0.1] - 2023-09-27 Creation of workflow for HiFi assembly with Hi-C phasing. 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 8901188dd..2df8c58ba 100644 --- a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md @@ -6,6 +6,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unreleased] +## [0.1.2] - 2023-11-07 +### Changed +- Added tag filtering for inputs + ## [0.1.1] - 2023-10-30 ### Changed - Names of the workflow and viles for consistency with other VGP workflows 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 47930adc2..a4073ec7a 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 @@ -14,7 +14,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.1.1", + "release": "0.1.2", "name": "kmer-profiling-hifi-VGP1", "steps": { "0": { @@ -33,8 +33,8 @@ "name": "Input dataset collection", "outputs": [], "position": { - "left": 25.07814953674619, - "top": 0 + "left": 0, + "top": 15.427657616021285 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}", @@ -60,8 +60,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 0, - "top": 290.01566057828205 + "left": 22.121832152706936, + "top": 151.04017592656817 }, "tool_id": null, "tool_state": "{\"default\": 21, \"parameter_type\": \"integer\", \"optional\": true}", @@ -87,8 +87,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 16.37496564855541, - "top": 493.99999877316264 + "left": 65.68433215270693, + "top": 283.0276637195369 }, "tool_id": null, "tool_state": "{\"default\": 2, \"parameter_type\": \"integer\", \"optional\": true}", @@ -123,8 +123,8 @@ } ], "position": { - "left": 326.0155759265076, - "top": 0.9843835878612026 + "left": 300.9374263897614, + "top": 16.412041203882488 }, "post_job_actions": { "HideDatasetActionread_db": { @@ -168,8 +168,8 @@ } ], "position": { - "left": 594.7968602779522, - "top": 127.82813604153586 + "left": 569.718710741206, + "top": 143.25579365755715 }, "post_job_actions": { "TagDatasetActionread_db": { @@ -221,8 +221,8 @@ } ], "position": { - "left": 884.453149536746, - "top": 76.92187131948805 + "left": 859.375, + "top": 92.34016036987308 }, "post_job_actions": { "HideDatasetActionread_db_hist": { @@ -298,8 +298,8 @@ } ], "position": { - "left": 1172.0166187911489, - "top": 96.88919830322266 + "left": 1198.9374694824219, + "top": 0.0 }, "post_job_actions": { "TagDatasetActionlinear_plot": { @@ -365,21 +365,6 @@ "uuid": "955de351-ef19-42dc-89d7-ca213994515a", "when": null, "workflow_outputs": [ - { - "label": "GenomeScope Model Parameters", - "output_name": "model_params", - "uuid": "cb88b945-413c-4e2d-81a9-dd838df902ff" - }, - { - "label": "GenomeScope log plot", - "output_name": "log_plot", - "uuid": "988e2189-d5f2-4e9e-8fc2-4434e68e8501" - }, - { - "label": "GenomeScope linear plot", - "output_name": "linear_plot", - "uuid": "57230be4-36d5-4307-b4b0-b8a73f6800ce" - }, { "label": "GenomeScope transformed linear plot", "output_name": "transformed_linear_plot", @@ -394,6 +379,21 @@ "label": "GenomeScope summary", "output_name": "summary", "uuid": "b74004e1-4f4b-4f43-a9f0-2a7a0a70ca1d" + }, + { + "label": "GenomeScope Model Parameters", + "output_name": "model_params", + "uuid": "cb88b945-413c-4e2d-81a9-dd838df902ff" + }, + { + "label": "GenomeScope log plot", + "output_name": "log_plot", + "uuid": "988e2189-d5f2-4e9e-8fc2-4434e68e8501" + }, + { + "label": "GenomeScope linear plot", + "output_name": "linear_plot", + "uuid": "57230be4-36d5-4307-b4b0-b8a73f6800ce" } ] } @@ -402,6 +402,6 @@ "Reviewed", "VGP" ], - "uuid": "3553367b-7f97-41e7-aa93-5856b21770df", - "version": 4 + "uuid": "a3ef9c73-c661-46af-bfde-3daa97d8b473", + "version": 2 } \ No newline at end of file