From 8485a84ff0f8873fa08fdde05697e4919b486399 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Wed, 24 Jul 2024 17:10:48 -0400 Subject: [PATCH] add report and fix assembly statistics --- .../CHANGELOG.md | 10 + .../Purging-duplicates-one-haplotype-VGP6b.ga | 581 +++++++++++++++--- 2 files changed, 496 insertions(+), 95 deletions(-) diff --git a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md index f587eae87..9fa769d3a 100644 --- a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md @@ -1,5 +1,15 @@ # Changelog +## [0.7] 2024-07-24 + +### Added + +- Workflow report + +### Changed + +- Fix bug where the columns of the assembly statistics didn't join properly. + ## [0.6] 2024-04-23 ### Changed diff --git a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b.ga b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b.ga index db9d55c79..84d47511f 100644 --- a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b.ga +++ b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b.ga @@ -15,8 +15,11 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.6", + "release": "0.7", "name": "Purging-duplicates-one-haplotype-VGP6b ", + "report": { + "markdown": "\n# Workflow Execution Report\n\nTime workflow was invoked\n\n```galaxy\ninvocation_time()\n```\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Merqury results\n\nMerqury QV:\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_QV\")\n```\n\nMerqury completeness:\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_stats\")\n```\n\nMerqury plots:\n\nspectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-cn.fl\")\n```\n\n\nspectra-asm:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-asm.fl\")\n```\n\n\nhap1 spectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_01.spectra-cn.fl\")\n```\n\n\nhap2 spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_02.spectra-cn.fl\")\n```\n\n\n\n\n## BUSCO results (Vertebrata database)\n\nPurged Assembly\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco on Purged Primary assembly: summary image\")\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": "", @@ -35,7 +38,7 @@ "outputs": [], "position": { "left": 0, - "top": 73.94776585535702 + "top": 473.0537740808015 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -62,7 +65,7 @@ "outputs": [], "position": { "left": 558.0468791193098, - "top": 445.9442866309247 + "top": 845.0502948563692 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}", @@ -89,7 +92,7 @@ "outputs": [], "position": { "left": 432.94921875, - "top": 976.4234574650022 + "top": 1375.5294656904466 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": \"\"}", @@ -116,7 +119,7 @@ "outputs": [], "position": { "left": 1972.4566892558003, - "top": 308.9738000531734 + "top": 708.0798082786179 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -135,15 +138,15 @@ "inputs": [ { "description": "", - "name": "Assembly to leave alone (need this for merqury)" + "name": "Assembly to leave alone (For Merqury comparison)" } ], - "label": "Assembly to leave alone (need this for merqury)", + "label": "Assembly to leave alone (For Merqury comparison)", "name": "Input dataset", "outputs": [], "position": { "left": 1972.4566892558003, - "top": 428.92176735660996 + "top": 828.0277755820543 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -170,7 +173,7 @@ "outputs": [], "position": { "left": 1693.6113702942387, - "top": 1098.9651229518047 + "top": 1498.071131177249 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -189,21 +192,21 @@ "inputs": [ { "description": "", - "name": "Name of un-altered assembly" + "name": "Name of purged assembly" } ], - "label": "Name of un-altered assembly", + "label": "Name of purged assembly", "name": "Input parameter", "outputs": [], "position": { - "left": 2540.373300171866, - "top": 399.9460505318975 + "left": 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