From a7c733d79c189956248290516420d603d407db7d Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Tue, 13 Aug 2024 12:21:36 -0400 Subject: [PATCH] expose busco lineage database parameter --- .../Scaffolding-HiC-VGP8/CHANGELOG.md | 4 + .../Scaffolding-HiC-VGP8/README.md | 11 +- .../Scaffolding-HiC-VGP8-tests.yml | 1 + .../Scaffolding-HiC-VGP8.ga | 293 +++++++++--------- 4 files changed, 162 insertions(+), 147 deletions(-) diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md index c7ad7943e..b801366da 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md @@ -1,5 +1,9 @@ # Changelog +## [0.2.7] 2024-08-13 + +- Expose Busco lineage database parameter + ## [0.2.6] 2024-08-05 ### Automatic update diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/README.md b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/README.md index 16413b667..6b8eee774 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/README.md +++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/README.md @@ -10,10 +10,13 @@ Example of trajectory : ## Inputs 1. Scaffolded assembly [fasta] -2. Concatenated HiC forward reads [fastq] -3. Concatenated HiC reverse reads [fastq] -4. Restriction enzyme sequence [txt] -5. Estimated genome size [txt] +2. Database for busco lineage (recommended: latest) +3. Busco lineage (recommended: vertebrata) +4. Concatenated HiC forward reads [fastq] +5. Concatenated HiC reverse reads [fastq] +6. Restriction enzyme sequence (recommended for VGP data: Arima Hi-C 2.0) +7. Estimated genome size [txt] + ### Outputs diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8-tests.yml b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8-tests.yml index 638d990be..b56a3c601 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8-tests.yml +++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8-tests.yml @@ -16,6 +16,7 @@ class: File location: https://zenodo.org/records/10037496/files/Estimated%20genome%20size%20-%20Parameter%20File.txt?download=1 filetype: txt + Database for Busco Lineage: v5 Lineage: vertebrata_odb10 Restriction enzymes: arima2 outputs: diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga index 4f291a9cb..deccec3a4 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga +++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga @@ -15,7 +15,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.2.6", + "release": "0.2.7", "name": "Scaffolding-HiC-VGP8", "report": { "markdown": "# Workflow Execution Report\n\nTime workflow was invoked\n\n```galaxy\ninvocation_time()\n```\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n\n## BUSCO results (Vertebrata database)\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco 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## PretextMap\n\n### Before Scaffolding\n\n\r\n```galaxy\nhistory_dataset_as_image(output=\"Pretext Map Before HiC scaffolding\")\n```\r\n\n\n### After Scaffolding\r\n```galaxy\nhistory_dataset_as_image(output=\"Pretext Map After HiC scaffolding\")\n```\r\n\n\n\n\n## Current Workflow\n```galaxy\nworkflow_display()\n```\n" @@ -73,19 +73,40 @@ "type": "data_input", "uuid": "13cd4c1c-968b-4077-9845-e06738a2efb8", "when": null, - "workflow_outputs": [ + "workflow_outputs": [] + }, + "2": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ { - "label": null, - "output_name": "output", - "uuid": "bd94bf34-0ed3-42f3-888d-36a56e74ff5b" + "description": "", + "name": "Database for Busco Lineage" } - ] + ], + "label": "Database for Busco Lineage", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 68.35425980970838, + "top": 413.51555364806376 + }, + "tool_id": null, + "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "1f4997fc-1880-4416-8857-2a63d3501a6c", + "when": null, + "workflow_outputs": [] }, - "2": { + "3": { "annotation": "Taxonomic lineage for the organism being assembled for Busco analysis\n", "content_id": null, "errors": null, - "id": 2, + "id": 3, "input_connections": {}, "inputs": [ { @@ -97,8 +118,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 89.68318337500133, - "top": 487.5 + "left": 84.74928132295123, + "top": 500.658153734641 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", @@ -106,19 +127,13 @@ "type": "parameter_input", "uuid": "b45e6bda-be0e-45e7-a9b1-17325a08dd76", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "18fe353c-d723-4118-a78c-f3237fe81064" - } - ] + "workflow_outputs": [] }, - "3": { + "4": { "annotation": "Forward reads as a single dataset in fastq format", "content_id": null, "errors": null, - "id": 3, + "id": 4, "input_connections": {}, "inputs": [ { @@ -141,11 +156,11 @@ "when": null, "workflow_outputs": [] }, - "4": { + "5": { "annotation": "Reverse reads as a single dataset in fastq format", "content_id": null, "errors": null, - "id": 4, + "id": 5, "input_connections": {}, "inputs": [ { @@ -168,11 +183,11 @@ "when": null, "workflow_outputs": [] }, - "5": { + "6": { "annotation": "Restriction enzymes used in preparation of Hi-C libraries.", "content_id": null, "errors": null, - "id": 5, + "id": 6, "input_connections": {}, "inputs": [ { @@ -193,19 +208,13 @@ "type": "parameter_input", "uuid": "b899a210-60c2-4e9e-8a34-e1bc82ef373d", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "05045d94-abce-486e-b4d7-8760cdcb4c96" - } - ] + "workflow_outputs": [] }, - "6": { + "7": { "annotation": "Estimated genome size from contiging workflow", "content_id": null, "errors": null, - "id": 6, + "id": 7, "input_connections": {}, "inputs": [ { @@ -228,11 +237,11 @@ "when": null, "workflow_outputs": [] }, - "7": { + "8": { "annotation": "", "content_id": null, "errors": null, - "id": 7, + "id": 8, "input_connections": {}, "inputs": [ { @@ -253,22 +262,16 @@ "type": "data_input", "uuid": "bc993517-ae23-417d-8eb1-891a127f544c", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "e3d9a2a4-63b2-48fa-9584-6430dcd538da" - } - ] + "workflow_outputs": [] }, - "8": { + "9": { "annotation": "", "content_id": "param_value_from_file", "errors": null, - "id": 8, + "id": 9, "input_connections": { "input1": { - "id": 6, + "id": 7, "output_name": "output" } }, @@ -300,18 +303,18 @@ "when": null, "workflow_outputs": [] }, - "9": { + "10": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 9, + "id": 10, "input_connections": { "input_file": { "id": 0, "output_name": "output" }, "mode_condition|swiss_army_knife": { - "id": 7, + "id": 8, "output_name": "output" } }, @@ -343,18 +346,18 @@ "when": null, "workflow_outputs": [] }, - "10": { + "11": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1", "errors": null, - "id": 10, + "id": 11, "input_connections": { "fastq_input|fastq_input1": { - "id": 3, + "id": 4, "output_name": "output" }, "reference_source|ref_file": { - "id": 9, + "id": 10, "output_name": "output" } }, @@ -392,18 +395,18 @@ "when": null, "workflow_outputs": [] }, - "11": { + "12": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1", "errors": null, - "id": 11, + "id": 12, "input_connections": { "fastq_input|fastq_input1": { - "id": 4, + "id": 5, "output_name": "output" }, "reference_source|ref_file": { - "id": 9, + "id": 10, "output_name": "output" } }, @@ -441,18 +444,18 @@ "when": null, "workflow_outputs": [] }, - "12": { + "13": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1", "errors": null, - "id": 12, + "id": 13, "input_connections": { "forward": { - "id": 10, + "id": 11, "output_name": "bam_output" }, "reverse": { - "id": 11, + "id": 12, "output_name": "bam_output" } }, @@ -492,14 +495,14 @@ "when": null, "workflow_outputs": [] }, - "13": { + "14": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1", "errors": null, - "id": 13, + "id": 14, "input_connections": { "input": { - "id": 12, + "id": 13, "output_name": "outfile" } }, @@ -539,26 +542,26 @@ "when": null, "workflow_outputs": [] }, - "14": { + "15": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy2", "errors": null, - "id": 14, + "id": 15, "input_connections": { "function|agp": { "id": 1, "output_name": "output" }, "function|bfile": { - "id": 12, + "id": 13, "output_name": "outfile" }, "function|enzyme_conditional|preconfigured_enzymes": { - "id": 5, + "id": 6, "output_name": "output" }, "function|fasta": { - "id": 9, + "id": 10, "output_name": "output" } }, @@ -638,14 +641,14 @@ } ] }, - "15": { + "16": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2", "errors": null, - "id": 15, + "id": 16, "input_connections": { "input": { - "id": 13, + "id": 14, "output_name": "pretext_map_out" } }, @@ -690,18 +693,18 @@ "when": null, "workflow_outputs": [] }, - "16": { + "17": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 16, + "id": 17, "input_connections": { "input_file": { - "id": 9, + "id": 10, "output_name": "output" }, "mode_condition|agp_to_path": { - "id": 14, + "id": 15, "output_name": "final_agp_out" } }, @@ -754,14 +757,14 @@ } ] }, - "17": { + "18": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 17, + "id": 18, "input_connections": { "input": { - "id": 15, + "id": 16, "output_name": "pretext_snap_out" } }, @@ -801,18 +804,18 @@ } ] }, - "18": { + "19": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 18, + "id": 19, "input_connections": { "input_file": { - "id": 16, + "id": 17, "output_name": "output" }, "mode_condition|swiss_army_knife": { - "id": 7, + "id": 8, "output_name": "output" } }, @@ -858,18 +861,18 @@ } ] }, - "19": { + "20": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 19, + "id": 20, "input_connections": { "input_file": { - "id": 16, + "id": 17, "output_name": "output" }, "mode_condition|statistics_condition|expected_genomesize": { - "id": 8, + "id": 9, "output_name": "integer_param" } }, @@ -915,14 +918,14 @@ } ] }, - "20": { + "21": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 20, + "id": 21, "input_connections": { "input_file": { - "id": 16, + "id": 17, "output_name": "output" } }, @@ -968,18 +971,18 @@ } ] }, - "21": { + "22": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1", "errors": null, - "id": 21, + "id": 22, "input_connections": { "fastq_input|fastq_input1": { - "id": 3, + "id": 4, "output_name": "output" }, "reference_source|ref_file": { - "id": 18, + "id": 19, "output_name": "output" } }, @@ -1017,18 +1020,18 @@ "when": null, "workflow_outputs": [] }, - "22": { + "23": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1", "errors": null, - "id": 22, + "id": 23, "input_connections": { "fastq_input|fastq_input1": { - "id": 4, + "id": 5, "output_name": "output" }, "reference_source|ref_file": { - "id": 18, + "id": 19, "output_name": "output" } }, @@ -1066,19 +1069,23 @@ "when": null, "workflow_outputs": [] }, - "23": { + "24": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0", "errors": null, - "id": 23, + "id": 24, "input_connections": { "input": { - "id": 18, + "id": 19, "output_name": "output" }, - "lineage|lineage_dataset": { + "lineage_conditional|cached_db": { "id": 2, "output_name": "output" + }, + "lineage|lineage_dataset": { + "id": 3, + "output_name": "output" } }, "inputs": [], @@ -1103,8 +1110,8 @@ } ], "position": { - "left": 3784.714433375001, - "top": 276.07421875 + "left": 3784.7033413689933, + "top": 244.7633599511914 }, "post_job_actions": { "TagDatasetActionbusco_missing": { @@ -1143,7 +1150,7 @@ "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\"], \"__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__\": \"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\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "5.5.0+galaxy0", "type": "tool", "uuid": "c30b907f-05c9-4709-a939-b66f52daf6e4", @@ -1161,14 +1168,14 @@ } ] }, - "24": { + "25": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "errors": null, - "id": 24, + "id": 25, "input_connections": { "infile": { - "id": 19, + "id": 20, "output_name": "stats" } }, @@ -1212,12 +1219,12 @@ } ] }, - "25": { + "26": { "annotation": "", - "id": 25, + "id": 26, "input_connections": { "gfa_stats": { - "id": 20, + "id": 21, "input_subworkflow_step_id": 0, "output_name": "stats" } @@ -1583,18 +1590,18 @@ "when": null, "workflow_outputs": [] }, - "26": { + "27": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1", "errors": null, - "id": 26, + "id": 27, "input_connections": { "forward": { - "id": 21, + "id": 22, "output_name": "bam_output" }, "reverse": { - "id": 22, + "id": 23, "output_name": "bam_output" } }, @@ -1634,14 +1641,14 @@ "when": null, "workflow_outputs": [] }, - "27": { + "28": { "annotation": "", "content_id": "Cut1", "errors": null, - "id": 27, + "id": 28, "input_connections": { "input": { - "id": 25, + "id": 26, "output_name": "gfastats data for plotting" } }, @@ -1667,14 +1674,14 @@ "when": null, "workflow_outputs": [] }, - "28": { + "29": { "annotation": "", "content_id": "Cut1", "errors": null, - "id": 28, + "id": 29, "input_connections": { "input": { - "id": 25, + "id": 26, "output_name": "gfastats data for plotting" } }, @@ -1706,14 +1713,14 @@ "when": null, "workflow_outputs": [] }, - "29": { + "30": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1", "errors": null, - "id": 29, + "id": 30, "input_connections": { "input": { - "id": 26, + "id": 27, "output_name": "outfile" } }, @@ -1753,14 +1760,14 @@ "when": null, "workflow_outputs": [] }, - "30": { + "31": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0", "errors": null, - "id": 30, + "id": 31, "input_connections": { "input": { - "id": 26, + "id": 27, "output_name": "outfile" } }, @@ -1798,14 +1805,14 @@ "when": null, "workflow_outputs": [] }, - "31": { + "32": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1", "errors": null, - "id": 31, + "id": 32, "input_connections": { "input1": { - "id": 27, + "id": 28, "output_name": "out_file1" } }, @@ -1858,14 +1865,14 @@ } ] }, - "32": { + "33": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1", "errors": null, - "id": 32, + "id": 33, "input_connections": { "input1": { - "id": 28, + "id": 29, "output_name": "out_file1" } }, @@ -1918,14 +1925,14 @@ } ] }, - "33": { + "34": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2", "errors": null, - "id": 33, + "id": 34, "input_connections": { "input": { - "id": 29, + "id": 30, "output_name": "pretext_map_out" } }, @@ -1970,14 +1977,14 @@ "when": null, "workflow_outputs": [] }, - "34": { + "35": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1", "errors": null, - "id": 34, + "id": 35, "input_connections": { "infile": { - "id": 30, + "id": 31, "output_name": "output" } }, @@ -2017,14 +2024,14 @@ "when": null, "workflow_outputs": [] }, - "35": { + "36": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 35, + "id": 36, "input_connections": { "input": { - "id": 33, + "id": 34, "output_name": "pretext_snap_out" } }, @@ -2068,6 +2075,6 @@ "tags": [ "VGP_curated" ], - "uuid": "88cb8c3c-791b-4ab8-b982-4811f6f94630", - "version": 5 -} + "uuid": "745110d9-a4ab-452e-b49a-7ee72f626975", + "version": 1 +} \ No newline at end of file