diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 495f5a1fd..7f5f6406e 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -5,6 +5,7 @@ FOR CONTRIBUTOR: FOR REVIEWERS: * [ ] .dockstore.yml: file is present and aligned with creator metadata in workflow. ORCID identifiers are strongly encouraged in creator metadata. The .dockstore.yml file is required to run tests +* [ ] Workflow is sufficiently generic to be used with lab data and does not hardcode sample names, reference data and can be run without reading an accompanying tutorial. * [ ] In workflow: annotation field contains short description of what the workflow does. Should start with `This workflow does/runs/performs … xyz … to generate/analyze/etc …` * [ ] In workflow: workflow inputs and outputs have human readable names (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless it is generally understood. Altering input or output labels requires adjusting these labels in the the workflow-tests.yml file as well * [ ] In workflow: `name` field should be human readable (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless generally understood diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 4407ee5b3..d77a6cbd4 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -7,7 +7,7 @@ on: types: [run-all-workflow-tests-command] env: GALAXY_FORK: galaxyproject - GALAXY_BRANCH: release_24.0 + GALAXY_BRANCH: release_24.1 MAX_CHUNKS: 40 jobs: setup: diff --git a/.github/workflows/workflow_test.yml b/.github/workflows/workflow_test.yml index 058498d07..a06b558d1 100644 --- a/.github/workflows/workflow_test.yml +++ b/.github/workflows/workflow_test.yml @@ -22,7 +22,7 @@ jobs: python-version-list: "[\"3.11\"]" max-chunks: 4 galaxy-fork: galaxyproject - galaxy-branch: release_24.0 + galaxy-branch: release_24.1 # Planemo lint the changed repositories lint: @@ -69,7 +69,7 @@ jobs: python-version-list: "[\"3.11\"]" repository-list: ${{ needs.setup.outputs.repository-list }} galaxy-fork: galaxyproject - galaxy-branch: release_24.0 + galaxy-branch: release_24.1 check-outputs: false combine_outputs: diff --git a/.gitignore b/.gitignore index 1bd11b884..447ea2d3e 100644 --- a/.gitignore +++ b/.gitignore @@ -3,3 +3,4 @@ tool_test_output.json .DS_Store workflow_manifest.json .vscode +*_diagrams.md diff --git a/README.md b/README.md index bd9a700c1..47fd5a8a2 100644 --- a/README.md +++ b/README.md @@ -34,7 +34,7 @@ All IWC workflows are automatically installed onto usegalaxy.* servers (i.e. [Ga ## Contributing a Workflow -Anyone can contribute a Galaxy Workflow. Please check out the [Adding workflow guidelines](workflows/README.md#adding-workflows). +Anyone can contribute a production Galaxy Workflow. Please check out the [Adding workflow guidelines](workflows/README.md#adding-workflows). If linting passes, tests pass, and human review passes, the PR is merged and diff --git a/workflows/README.md b/workflows/README.md index 9a94d2d40..77cd7c0c5 100644 --- a/workflows/README.md +++ b/workflows/README.md @@ -19,6 +19,17 @@ The structure is as follows: ## Adding workflows +### Workflow eligibility + +We want to collect production workflows targeted at users that want to analyze their own data. +As such, the workflow should be sufficiently generic that users can provide their own data. + +We encourage, but do not require, links to related [Galaxy Training Network Tutorials](https://training.galaxyproject.org/). +Importantly, each workflow should be described in a way that a user can run the +workflow on their own data without modifying the workflow. If you wish to +deposit a workflow that accompanies a tutorial please make sure that the workflow +does not refer to datasets that only make sense in the context of the tutorial. + Here are some guidelines to help new contributors to add their workflows. Everything starts from a workflow that you have on a galaxy instance. 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 90391a239..f68fbb603 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": "0.3", + "release": "0.4", "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" @@ -1178,7 +1178,7 @@ }, "30": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "errors": null, "id": 30, "input_connections": { @@ -1220,15 +1220,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "f4a3eff8ab85", + "changeset_revision": "764f2516d837", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"no\", \"__current_case__\": 0}}, \"discover_paths\": true, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.9+galaxy0", + "tool_version": "1.3.9+galaxy1", "type": "tool", "uuid": "ae31efe9-7f56-4a2d-b811-d77d4f8b0abf", "when": null, @@ -1242,7 +1242,7 @@ }, "31": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "errors": null, "id": 31, "input_connections": { @@ -1284,15 +1284,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "f4a3eff8ab85", + "changeset_revision": "764f2516d837", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"no\", \"__current_case__\": 0}}, \"discover_paths\": true, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.9+galaxy0", + "tool_version": "1.3.9+galaxy1", "type": "tool", "uuid": "f2a02b12-43b7-4969-a999-dbc18b820c2f", "when": null, @@ -1359,7 +1359,7 @@ }, "33": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "errors": null, "id": 33, "input_connections": { @@ -1415,15 +1415,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "f4a3eff8ab85", + "changeset_revision": "764f2516d837", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"fasta\", \"__current_case__\": 0, \"line_length\": null}, \"discover_paths\": true, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.9+galaxy0", + "tool_version": "1.3.9+galaxy1", "type": "tool", "uuid": "653200d3-c548-4dd2-87cb-e8b40fbc8235", "when": null, @@ -1437,7 +1437,7 @@ }, "34": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "errors": null, "id": 34, "input_connections": { @@ -1493,15 +1493,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "f4a3eff8ab85", + "changeset_revision": "764f2516d837", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"fasta\", \"__current_case__\": 0, \"line_length\": null}, \"discover_paths\": true, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.9+galaxy0", + "tool_version": "1.3.9+galaxy1", "type": "tool", "uuid": "77c35546-0668-45d5-aa10-2c5048fd4256", "when": null, @@ -1515,7 +1515,7 @@ }, "35": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "errors": null, "id": 35, "input_connections": { @@ -1546,15 +1546,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "f4a3eff8ab85", + "changeset_revision": "764f2516d837", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"size\", \"__current_case__\": 0, \"out_size\": \"c\"}, \"locale\": false, \"tabular\": true, \"discover_paths\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.9+galaxy0", + "tool_version": "1.3.9+galaxy1", "type": "tool", "uuid": "fb185c69-e1a1-47a4-b983-d25d94f25522", "when": null, @@ -1562,7 +1562,7 @@ }, "36": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "errors": null, "id": 36, "input_connections": { @@ -1593,15 +1593,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "f4a3eff8ab85", + "changeset_revision": "764f2516d837", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"size\", \"__current_case__\": 0, \"out_size\": \"c\"}, \"locale\": false, \"tabular\": true, \"discover_paths\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.9+galaxy0", + "tool_version": "1.3.9+galaxy1", "type": "tool", "uuid": "a3de4200-b7d2-4cd5-bcca-fa6f548ed6a0", "when": null, @@ -1609,7 +1609,7 @@ }, "37": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "errors": null, "id": 37, "input_connections": { @@ -1644,15 +1644,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "f4a3eff8ab85", + "changeset_revision": "764f2516d837", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"assembly\", \"__current_case__\": 2, \"expected_genomesize\": {\"__class__\": \"ConnectedValue\"}}, \"locale\": true, \"tabular\": true, \"discover_paths\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.9+galaxy0", + "tool_version": "1.3.9+galaxy1", "type": "tool", "uuid": "60492710-1411-45ff-abe6-1c94644bcca4", "when": null, @@ -1660,7 +1660,7 @@ }, "38": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "errors": null, "id": 38, "input_connections": { @@ -1695,15 +1695,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "f4a3eff8ab85", + "changeset_revision": "764f2516d837", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"assembly\", \"__current_case__\": 2, \"expected_genomesize\": {\"__class__\": \"ConnectedValue\"}}, \"locale\": true, \"tabular\": true, \"discover_paths\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.9+galaxy0", + "tool_version": "1.3.9+galaxy1", "type": "tool", "uuid": "904feec3-140a-4aff-a8af-29592733175e", "when": null, @@ -1801,7 +1801,7 @@ "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, \"use_augustus\": {\"use_augustus_selector\": \"metaeuk\", \"__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_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"metaeuk\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"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": "5.8.0+galaxy0", "type": "tool", "uuid": "bc06da8e-e5cb-493e-98d1-c974a3e46cff", @@ -1916,7 +1916,7 @@ "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, \"use_augustus\": {\"use_augustus_selector\": \"metaeuk\", \"__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_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"metaeuk\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"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": "5.8.0+galaxy0", "type": "tool", "uuid": "4931c626-b636-43c3-b19b-3c778199b9a8", @@ -2467,7 +2467,7 @@ } }, "tags": [], - "uuid": "0db8092c-fa2f-4780-97e9-eddf9381a024" + "uuid": "857e24f8-fb7a-4a3f-a55c-aea22e32a282" }, "tool_id": null, "type": "subworkflow", @@ -2849,7 +2849,7 @@ } }, "tags": [], - "uuid": "89293c64-2b08-41e3-912f-e3c226047551" + "uuid": "cd145237-3c4a-400d-90d4-9603f3098ce6" }, "tool_id": null, "type": "subworkflow", @@ -3741,7 +3741,7 @@ } }, "tags": [], - "uuid": "b78e621c-7220-413c-bf73-7109f9bd1e62" + "uuid": "37bb5ce3-a485-4340-b37a-7f3ab5c655fa" }, "tool_id": null, "type": "subworkflow", 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 bdeb6cb38..17d779188 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 +1,10 @@ # Changelog +## [0.4] 2024-12-16 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1` + ## [0.3] 2024-11-11 ### Automatic update 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 8d550d3e8..c617502d7 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 +1,8 @@ # Changelog +## [0.1.9] 2024-12-17 +### Added +- Annotation for workflow describing its function ## [0.1.8] 2024-12-03 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 3f79a85b4..8dbe5c31f 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 @@ -29,16 +29,16 @@ delta: 10000 GenomeScope summary: asserts: - has_text: - text: '27,842 bp' - has_text: - text: '35,913 bp' + - has_text_matching: + expression: '27,84. bp' + - has_text_matching: + expression: '35,91. bp' GenomeScope Model Parameters: asserts: - has_text: - text: '0.0918418396430493' - has_text: - text: '27.44263' + - has_text_matching: + expression: '0.09184.*' + - has_text_matching: + expression: '27.44.*' Merged Meryl Database: asserts: has_size: 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 5c393fb3d..a57db03d4 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 @@ -1,6 +1,6 @@ { "a_galaxy_workflow": "true", - "annotation": "", + "annotation": "Performs k-mer profiling on PacBio data and generates GenomeScope plots and summary for genome characteristics assessment.", "comments": [], "creator": [ { @@ -15,7 +15,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.1.8", + "release": "0.1.9", "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"