From 0197b236ef92280087068591b75c18154c5e1ca5 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Wed, 11 Dec 2024 15:43:28 +0100 Subject: [PATCH 1/8] Clarify that IWC aims to provide production workflows --- .github/PULL_REQUEST_TEMPLATE.md | 1 + README.md | 2 +- workflows/README.md | 11 +++++++++++ 3 files changed, 13 insertions(+), 1 deletion(-) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 495f5a1fd3..7f5f6406e1 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/README.md b/README.md index bd9a700c19..47fd5a8a21 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 9a94d2d40a..77cd7c0c54 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. From 7c7c34110796e3e8cc5824d1422348d7fa394dec Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Fri, 13 Dec 2024 15:50:10 +0100 Subject: [PATCH 2/8] Bump tests to run against 24.1 --- .github/workflows/ci.yaml | 2 +- .github/workflows/workflow_test.yml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 4407ee5b30..d77a6cbd49 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 058498d078..a06b558d17 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: From f490bbaf4fe4144ca15f2f4c3413333e9c252317 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 16 Dec 2024 04:31:51 +0000 Subject: [PATCH 3/8] Updating workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5 from 0.3 to 0.4 --- .../Assembly-Hifi-Trio-phasing-VGP5.ga | 165 +++++++++++++----- .../CHANGELOG.md | 5 + 2 files changed, 122 insertions(+), 48 deletions(-) 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 90391a2399..401cd50e2f 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" @@ -464,7 +464,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cutadapt", + "name": "library" + } + ], "label": null, "name": "Cutadapt", "outputs": [ @@ -1031,7 +1036,20 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Hifiasm", + "name": "assembly_options" + }, + { + "description": "runtime parameter for tool Hifiasm", + "name": "mode" + }, + { + "description": "runtime parameter for tool Hifiasm", + "name": "mode" + } + ], "label": null, "name": "Hifiasm", "outputs": [ @@ -1178,7 +1196,7 @@ }, "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": { @@ -1191,7 +1209,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1220,15 +1243,15 @@ "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 +1265,7 @@ }, "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": { @@ -1255,7 +1278,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1284,15 +1312,15 @@ "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 +1387,7 @@ }, "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": { @@ -1372,7 +1400,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1415,15 +1448,15 @@ "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 +1470,7 @@ }, "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": { @@ -1450,7 +1483,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1493,15 +1531,15 @@ "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 +1553,7 @@ }, "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 +1584,15 @@ "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 +1600,7 @@ }, "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 +1631,15 @@ "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 +1647,7 @@ }, "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 +1682,15 @@ "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 +1698,7 @@ }, "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 +1733,15 @@ "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, @@ -1728,7 +1766,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Busco", + "name": "lineage" + }, + { + "description": "runtime parameter for tool Busco", + "name": "lineage_conditional" + } + ], "label": null, "name": "Busco", "outputs": [ @@ -1801,7 +1848,7 @@ "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", @@ -1843,7 +1890,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Busco", + "name": "lineage" + }, + { + "description": "runtime parameter for tool Busco", + "name": "lineage_conditional" + } + ], "label": null, "name": "Busco", "outputs": [ @@ -1916,7 +1972,7 @@ "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", @@ -1966,7 +2022,20 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Merqury", + "name": "mode" + }, + { + "description": "runtime parameter for tool Merqury", + "name": "mode" + }, + { + "description": "runtime parameter for tool Merqury", + "name": "mode" + } + ], "label": null, "name": "Merqury", "outputs": [ @@ -2467,7 +2536,7 @@ } }, "tags": [], - "uuid": "0db8092c-fa2f-4780-97e9-eddf9381a024" + "uuid": "857e24f8-fb7a-4a3f-a55c-aea22e32a282" }, "tool_id": null, "type": "subworkflow", @@ -2849,7 +2918,7 @@ } }, "tags": [], - "uuid": "89293c64-2b08-41e3-912f-e3c226047551" + "uuid": "cd145237-3c4a-400d-90d4-9603f3098ce6" }, "tool_id": null, "type": "subworkflow", @@ -3741,7 +3810,7 @@ } }, "tags": [], - "uuid": "b78e621c-7220-413c-bf73-7109f9bd1e62" + "uuid": "37bb5ce3-a485-4340-b37a-7f3ab5c655fa" }, "tool_id": null, "type": "subworkflow", @@ -3921,4 +3990,4 @@ ], "uuid": "bd09a130-801c-4cb8-b848-ab90b3161322", "version": 3 -} +} \ 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 bdeb6cb38e..17d779188b 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 From f874fb677a1240ac28d1d13af97b37dd8df35545 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Mon, 16 Dec 2024 08:15:06 -0500 Subject: [PATCH 4/8] Add *_diagrams.md to .gitignore. These *could* be included in the repo, though, if we want? --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index 1bd11b8849..447ea2d3e2 100644 --- a/.gitignore +++ b/.gitignore @@ -3,3 +3,4 @@ tool_test_output.json .DS_Store workflow_manifest.json .vscode +*_diagrams.md From f56cb89bd6c005c554131f02b054361dd09519b7 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Mon, 16 Dec 2024 15:47:00 -0500 Subject: [PATCH 5/8] remove runtime parameters --- .../Assembly-Hifi-Trio-phasing-VGP5.ga | 89 +++---------------- 1 file changed, 10 insertions(+), 79 deletions(-) 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 401cd50e2f..f68fbb603c 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 @@ -464,12 +464,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Cutadapt", - "name": "library" - } - ], + "inputs": [], "label": null, "name": "Cutadapt", "outputs": [ @@ -1036,20 +1031,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Hifiasm", - "name": "assembly_options" - }, - { - "description": "runtime parameter for tool Hifiasm", - "name": "mode" - }, - { - "description": "runtime parameter for tool Hifiasm", - "name": "mode" - } - ], + "inputs": [], "label": null, "name": "Hifiasm", "outputs": [ @@ -1209,12 +1191,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -1278,12 +1255,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -1400,12 +1372,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -1483,12 +1450,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -1766,16 +1728,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Busco", - "name": "lineage" - }, - { - "description": "runtime parameter for tool Busco", - "name": "lineage_conditional" - } - ], + "inputs": [], "label": null, "name": "Busco", "outputs": [ @@ -1890,16 +1843,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Busco", - "name": "lineage" - }, - { - "description": "runtime parameter for tool Busco", - "name": "lineage_conditional" - } - ], + "inputs": [], "label": null, "name": "Busco", "outputs": [ @@ -2022,20 +1966,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Merqury", - "name": "mode" - }, - { - "description": "runtime parameter for tool Merqury", - "name": "mode" - }, - { - "description": "runtime parameter for tool Merqury", - "name": "mode" - } - ], + "inputs": [], "label": null, "name": "Merqury", "outputs": [ @@ -3990,4 +3921,4 @@ ], "uuid": "bd09a130-801c-4cb8-b848-ab90b3161322", "version": 3 -} \ No newline at end of file +} From 86e1591853ca34698deda74b25b886bfc109967e Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Tue, 17 Dec 2024 09:57:23 -0500 Subject: [PATCH 6/8] Add annotation for vgp1 kmer profiling workflow --- .../kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 5c393fb3d8..161a72f104 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": [ { From 11147551921ba3b40949756f651b37ed9b684f7b Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Tue, 17 Dec 2024 11:09:43 -0500 Subject: [PATCH 7/8] Update changelog and increment version to 0.1.9; add workflow annotation --- .../VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md | 3 +++ .../kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) 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 8d550d3e80..c617502d7d 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.ga b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga index 161a72f104..a57db03d4a 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": "0.1.8", + "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" From 6acb4bd0fe6f8de3124a6bbc08194a7b74795b27 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Tue, 17 Dec 2024 17:29:39 +0100 Subject: [PATCH 8/8] Make test slightly more lentient --- .../kmer-profiling-hifi-VGP1-tests.yml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) 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 3f79a85b4b..8dbe5c31fd 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: