From 8e65bb0abecc4ef88888e1b4224c05bbe1b9f9b9 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Tue, 13 Aug 2024 12:06:17 -0400 Subject: [PATCH] add workflow report and expose busco database --- .../Assembly-Hifi-Trio-phasing-VGP5-tests.yml | 1 + .../Assembly-Hifi-Trio-phasing-VGP5.ga | 826 ++++++++++++++---- .../CHANGELOG.md | 13 + 3 files changed, 664 insertions(+), 176 deletions(-) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5-tests.yml b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5-tests.yml index 1300eae42..8b77724e8 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5-tests.yml +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5-tests.yml @@ -52,6 +52,7 @@ Bits for bloom filter: 32 Name for Haplotype 1: Hap1 Name for Haplotype 2: Hap2 + Database for Busco Lineage: v5 Lineage: vertebrata_odb10 outputs: Estimated Genome size: 2288021 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 f13aee696..d9b21ec9f 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 @@ -15,8 +15,11 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.1.8", + "release": "0.2", "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" + }, "steps": { "0": { "annotation": "", @@ -196,8 +199,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 16.973703852699934, - "top": 875.4758102675167 + "left": 14.278967454027603, + "top": 893.0522085856591 }, "tool_id": null, "tool_state": "{\"default\": 37, \"parameter_type\": \"integer\", \"optional\": true}", @@ -205,14 +208,53 @@ "type": "parameter_input", "uuid": "a5987ed3-6fdb-49c7-92d0-5b2f78a9bbb9", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "1bb5df96-d731-4e12-b902-ec6e1d723b07" + } + ] }, "7": { - "annotation": "Taxonomic lineage for the organism being assembled for Busco analysis", + "annotation": "", "content_id": null, "errors": null, "id": 7, "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Database for Busco Lineage" + } + ], + "label": "Database for Busco Lineage", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 28.142955132748718, + "top": 1078.9295496884674 + }, + "tool_id": null, + "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "ca553be3-e5c9-4770-bd61-d50ed05c69ae", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "9829d67c-d793-44c9-9b53-9c3ebd2155a8" + } + ] + }, + "8": { + "annotation": "Taxonomic lineage for the organism being assembled for Busco analysis", + "content_id": null, + "errors": null, + "id": 8, + "input_connections": {}, "inputs": [ { "description": "Taxonomic lineage for the organism being assembled for Busco analysis", @@ -223,8 +265,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 36.34366195032787, - "top": 998.1239416236981 + "left": 61.152110333438976, + "top": 1189.4200518565176 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", @@ -232,13 +274,19 @@ "type": "parameter_input", "uuid": "9762d451-eb6f-4f0c-8203-7094f46ea771", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "9dff2868-bf8a-4443-87c9-52f5b8975bdb" + } + ] }, - "8": { + "9": { "annotation": "If empty, read coverage will be estimated from the Genomescope parameters. ", "content_id": null, "errors": null, - "id": 8, + "id": 9, "input_connections": {}, "inputs": [ { @@ -250,8 +298,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 65.73786407849795, - "top": 1111.7501052118992 + "left": 98.92882500063175, + "top": 1275.4014318043698 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"integer\", \"optional\": true}", @@ -259,13 +307,19 @@ "type": "parameter_input", "uuid": "ffcf874f-594d-4d58-99dc-73ef566bcc88", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "28a260f0-a63e-4743-ba41-6544e4f423a9" + } + ] }, - "9": { + "10": { "annotation": "GenomeScope model parameters generated by K-mer profiling workflow", "content_id": null, "errors": null, - "id": 9, + "id": 10, "input_connections": {}, "inputs": [ { @@ -277,8 +331,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 101.3532659049146, - "top": 1219.9729028733702 + "left": 146.82808789081685, + "top": 1368.9007539001223 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", @@ -288,11 +342,11 @@ "when": null, "workflow_outputs": [] }, - "10": { + "11": { "annotation": "", "content_id": null, "errors": null, - "id": 10, + "id": 11, "input_connections": {}, "inputs": [ { @@ -304,8 +358,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 150.24297371017008, - "top": 1347.367362010912 + "left": 217.51082966945373, + "top": 1473.9095926545822 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", @@ -315,11 +369,11 @@ "when": null, "workflow_outputs": [] }, - "11": { + "12": { "annotation": "--trio-dual option", "content_id": null, "errors": null, - "id": 11, + "id": 12, "input_connections": {}, "inputs": [ { @@ -331,8 +385,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 227.5310800942477, - "top": 1472.080580726721 + "left": 306.5808483755939, + "top": 1565.8147646057243 }, "tool_id": null, "tool_state": "{\"default\": true, \"parameter_type\": \"boolean\", \"optional\": true}", @@ -340,13 +394,19 @@ "type": "parameter_input", "uuid": "eb8c0bcc-14c8-4b3d-b73f-442eae454b82", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "b178a102-00b1-45ae-8404-2c7c544cdeee" + } + ] }, - "12": { + "13": { "annotation": "", "content_id": null, "errors": null, - "id": 12, + "id": 13, "input_connections": {}, "inputs": [ { @@ -367,13 +427,19 @@ "type": "data_input", "uuid": "80ff22ac-1a58-4f89-bf52-48f18d8f71f9", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "c2cf45d3-af1d-49d6-9d77-41065f57fcdb" + } + ] }, - "13": { + "14": { "annotation": "", "content_id": null, "errors": null, - "id": 13, + "id": 14, "input_connections": {}, "inputs": [ { @@ -394,13 +460,19 @@ "type": "parameter_input", "uuid": "c5651e7e-31d4-41b7-a590-e2fadc7f59e9", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "ad235ad6-b670-4423-ac52-bbec7296f64a" + } + ] }, - "14": { + "15": { "annotation": "", "content_id": null, "errors": null, - "id": 14, + "id": 15, "input_connections": {}, "inputs": [ { @@ -421,13 +493,19 @@ "type": "parameter_input", "uuid": "1ae103f4-38e9-4414-8e46-b8a763159937", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "276bc5aa-1667-4b75-9dfa-52c1cea29d50" + } + ] }, - "15": { + "16": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "errors": null, - "id": 15, + "id": 16, "input_connections": { "library|input_1": { "id": 0, @@ -496,14 +574,14 @@ } ] }, - "16": { + "17": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0", "errors": null, - "id": 16, + "id": 17, "input_connections": { "input": { - "id": 9, + "id": 10, "output_name": "output" } }, @@ -541,14 +619,14 @@ "when": null, "workflow_outputs": [] }, - "17": { + "18": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1", "errors": null, - "id": 17, + "id": 18, "input_connections": { "infile": { - "id": 10, + "id": 11, "output_name": "output" } }, @@ -586,14 +664,14 @@ "when": null, "workflow_outputs": [] }, - "18": { + "19": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", "errors": null, - "id": 18, + "id": 19, "input_connections": { "results_0|software_cond|input": { - "id": 15, + "id": 16, "output_name": "report" } }, @@ -628,26 +706,26 @@ "uuid": "b64b5b58-cf21-4fb6-af57-2e8a56e85142", "when": null, "workflow_outputs": [ - { - "label": "multiqc html report", - "output_name": "html_report", - "uuid": "9bd9c4ff-97c3-4557-a550-a360207e08ab" - }, { "label": "cutadapt multiqc stats", "output_name": "stats", "uuid": "110b5141-3025-4ee6-8d4a-d4987fa6dfe5" + }, + { + "label": "multiqc html report", + "output_name": "html_report", + "uuid": "9bd9c4ff-97c3-4557-a550-a360207e08ab" } ] }, - "19": { + "20": { "annotation": "", "content_id": "Cut1", "errors": null, - "id": 19, + "id": 20, "input_connections": { "input": { - "id": 16, + "id": 17, "output_name": "out_file1" } }, @@ -679,14 +757,14 @@ "when": null, "workflow_outputs": [] }, - "20": { + "21": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "errors": null, - "id": 20, + "id": 21, "input_connections": { "infile": { - "id": 17, + "id": 18, "output_name": "output" } }, @@ -724,14 +802,14 @@ "when": null, "workflow_outputs": [] }, - "21": { + "22": { "annotation": "", "content_id": "param_value_from_file", "errors": null, - "id": 21, + "id": 22, "input_connections": { "input1": { - "id": 19, + "id": 20, "output_name": "out_file1" } }, @@ -763,14 +841,14 @@ "when": null, "workflow_outputs": [] }, - "22": { + "23": { "annotation": "", "content_id": "Convert characters1", "errors": null, - "id": 22, + "id": 23, "input_connections": { "input": { - "id": 20, + "id": 21, "output_name": "outfile" } }, @@ -802,18 +880,18 @@ "when": null, "workflow_outputs": [] }, - "23": { + "24": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, - "id": 23, + "id": 24, "input_connections": { "style_cond|type_cond|pick_from_0|value": { - "id": 8, + "id": 9, "output_name": "output" }, "style_cond|type_cond|pick_from_1|value": { - "id": 21, + "id": 22, "output_name": "integer_param" } }, @@ -853,14 +931,14 @@ "when": null, "workflow_outputs": [] }, - "24": { + "25": { "annotation": "", "content_id": "Cut1", "errors": null, - "id": 24, + "id": 25, "input_connections": { "input": { - "id": 22, + "id": 23, "output_name": "out_file1" } }, @@ -892,14 +970,14 @@ "when": null, "workflow_outputs": [] }, - "25": { + "26": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0", "errors": null, - "id": 25, + "id": 26, "input_connections": { "assembly_options|hom_cov": { - "id": 23, + "id": 24, "output_name": "integer_param" }, "filter_bits": { @@ -907,11 +985,11 @@ "output_name": "output" }, "mode|reads": { - "id": 15, + "id": 16, "output_name": "out1" }, "mode|trio_dual": { - "id": 11, + "id": 12, "output_name": "output" }, "mode|trioinput|hap1_reads": { @@ -1014,14 +1092,14 @@ "when": null, "workflow_outputs": [] }, - "26": { + "27": { "annotation": "", "content_id": "param_value_from_file", "errors": null, - "id": 26, + "id": 27, "input_connections": { "input1": { - "id": 24, + "id": 25, "output_name": "out_file1" } }, @@ -1068,18 +1146,18 @@ } ] }, - "27": { + "28": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 27, + "id": 28, "input_connections": { "input_file": { - "id": 25, + "id": 26, "output_name": "hap1_contigs" }, "mode_condition|swiss_army_knife": { - "id": 12, + "id": 13, "output_name": "output" } }, @@ -1132,18 +1210,18 @@ } ] }, - "28": { + "29": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 28, + "id": 29, "input_connections": { "input_file": { - "id": 25, + "id": 26, "output_name": "hap2_contigs" }, "mode_condition|swiss_army_knife": { - "id": 12, + "id": 13, "output_name": "output" } }, @@ -1196,14 +1274,14 @@ } ] }, - "29": { + "30": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4", "errors": null, - "id": 29, + "id": 30, "input_connections": { "input_file": { - "id": 25, + "id": 26, "output_name": "raw_unitigs_trio" } }, @@ -1241,20 +1319,26 @@ "type": "tool", "uuid": "f9af6aa8-4ee4-4d4d-a54f-653881706285", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": "raw unitig graph image", + "output_name": "outfile", + "uuid": "c5d8c5b8-3d33-473d-96bc-cedd33d14786" + } + ] }, - "30": { + "31": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 30, + "id": 31, "input_connections": { "input_file": { - "id": 25, + "id": 26, "output_name": "hap1_contigs" }, "mode_condition|swiss_army_knife": { - "id": 12, + "id": 13, "output_name": "output" } }, @@ -1321,18 +1405,18 @@ } ] }, - "31": { + "32": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 31, + "id": 32, "input_connections": { "input_file": { - "id": 25, + "id": 26, "output_name": "hap2_contigs" }, "mode_condition|swiss_army_knife": { - "id": 12, + "id": 13, "output_name": "output" } }, @@ -1399,14 +1483,14 @@ } ] }, - "32": { + "33": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 32, + "id": 33, "input_connections": { "input_file": { - "id": 25, + "id": 26, "output_name": "hap1_contigs" } }, @@ -1446,14 +1530,14 @@ "when": null, "workflow_outputs": [] }, - "33": { + "34": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 33, + "id": 34, "input_connections": { "input_file": { - "id": 25, + "id": 26, "output_name": "hap2_contigs" } }, @@ -1493,18 +1577,18 @@ "when": null, "workflow_outputs": [] }, - "34": { + "35": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 34, + "id": 35, "input_connections": { "input_file": { - "id": 25, + "id": 26, "output_name": "hap2_contigs" }, "mode_condition|statistics_condition|expected_genomesize": { - "id": 26, + "id": 27, "output_name": "integer_param" } }, @@ -1544,18 +1628,18 @@ "when": null, "workflow_outputs": [] }, - "35": { + "36": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 35, + "id": 36, "input_connections": { "input_file": { - "id": 25, + "id": 26, "output_name": "hap1_contigs" }, "mode_condition|statistics_condition|expected_genomesize": { - "id": 26, + "id": 27, "output_name": "integer_param" } }, @@ -1595,19 +1679,23 @@ "when": null, "workflow_outputs": [] }, - "36": { + "37": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0", "errors": null, - "id": 36, + "id": 37, "input_connections": { "input": { - "id": 30, + "id": 31, "output_name": "output" }, - "lineage|lineage_dataset": { + "lineage_conditional|cached_db": { "id": 7, "output_name": "output" + }, + "lineage|lineage_dataset": { + "id": 8, + "output_name": "output" } }, "inputs": [], @@ -1683,7 +1771,7 @@ "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, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"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, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": 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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 353004091..caa6d3c0e 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 +1,18 @@ # Changelog +## [0.2] 2024-08-12 + +### Added + +- Workflow report + +### Changed + +- Exposing the Busco lineage database parameter +- Fixing a bug happening when merging of assembly statistics + + + ## [0.1.8] 2024-07-22 ### Automatic update