From 9e571049c53a09e246c7433f2e25a0cbdda9ce66 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Thu, 1 Aug 2024 16:13:39 -0400 Subject: [PATCH] add worflow report --- .../Assembly-Hifi-only-VGP3-tests.yml | 4 + .../Assembly-Hifi-only-VGP3.ga | 578 +++++++++++++++--- .../Assembly-Hifi-only-VGP3/CHANGELOG.md | 11 + 3 files changed, 513 insertions(+), 80 deletions(-) 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..f8af1a040 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 @@ -44,6 +44,10 @@ 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..57d568faa 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", "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": "", @@ -124,7 +127,13 @@ "type": "parameter_input", "uuid": "3ce6ecc2-3262-4695-b4ef-1a58f52a48bd", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "66115e1f-5bbb-4d04-bf6a-5d4ed3dbd98b" + } + ] }, "4": { "annotation": "If empty, read coverage will be estimated from the Genomescope parameters. 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+ ], + "position": { + "left": 4748.6890863468225, + "top": 495.54555212695516 + }, + "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__\": \"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" + } + ] } }, "tags": [ "VGP", "Reviewed" ], - "uuid": "f6f4cac5-6900-440b-8f1d-52420f635420", - "version": 1 -} + "uuid": "39c93c40-5bcb-42f2-a12e-a4a4fae21ed7", + "version": 12 +} \ 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..38064d35b 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 +1,16 @@ # Changelog +## [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