diff --git a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md index c97185747..43b11af20 100644 --- a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [0.3.4] 2024-02-15 + +- Remove tag filtering +- Add merqury histogram outputs + ## [0.3.3] 2023-11-20 - Fix author in dockstore diff --git a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6.ga b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6.ga index ed0a9928f..08e1b4b05 100644 --- a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6.ga +++ b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6.ga @@ -1,6 +1,7 @@ { "a_galaxy_workflow": "true", "annotation": "Purge contigs marked as duplicates by purge_dups (could be haplotypic duplication or overlap duplication). This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5)", + "comments": [], "creator": [ { "class": "Organization", @@ -14,7 +15,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.3.3", + "release": "0.3.4", "name": "Purge-duplicate-contigs-VGP6", "steps": { "0": { @@ -37,7 +38,7 @@ "top": 0 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": \"trimmed_hifi\", \"collection_type\": \"list\"}", + "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}", "tool_version": null, "type": "data_collection_input", "uuid": "0df002ab-91cf-4767-a348-9ce31f439a01", @@ -64,7 +65,7 @@ "top": 101.30078125 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": \"hifiasm_hic_hap1\"}", + "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": \"\"}", "tool_version": null, "type": "data_input", "uuid": "158c873a-b3bc-4135-95d4-d435a4849786", @@ -91,7 +92,7 @@ "top": 200.42266845703125 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": \"hifiasm_hic_hap2\"}", + "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": \"\"}", "tool_version": null, "type": "data_input", "uuid": "681334cb-47f1-49cb-9f86-612e17655419", @@ -118,7 +119,7 @@ "top": 297.9609375 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": \"meryl_db\"}", + "tool_state": "{\"optional\": false, \"tag\": \"\"}", "tool_version": null, "type": "data_input", "uuid": "0c3b5f68-3534-4d76-b291-e844707606ec", @@ -141,11 +142,11 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 145.4080810546875, - "top": 390.35603841145866 + "left": 146.16796875, + "top": 390.59765625 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": \"genomescope_params\"}", + "tool_state": "{\"optional\": false, \"tag\": \"\"}", "tool_version": null, "type": "data_input", "uuid": "5c8af4f2-5764-49a6-89fa-dd8730b11828", @@ -172,7 +173,7 @@ "top": 507.23516845703125 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": \"estimated_genome_size\"}", + "tool_state": "{\"optional\": false, \"tag\": \"\"}", "tool_version": null, "type": "data_input", "uuid": "9cc9d8e4-a917-4258-a9fc-74de593c42de", @@ -302,7 +303,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Map with minimap2", + "name": "fastq_input" + }, + { + "description": "runtime parameter for tool Map with minimap2", + "name": "reference_source" + } + ], "label": null, "name": "Map with minimap2", "outputs": [ @@ -354,7 +364,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + } + ], "label": null, "name": "Purge overlaps", "outputs": [ @@ -399,7 +414,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Compute", + "name": "input" + } + ], "label": null, "name": "Compute", "outputs": [ @@ -444,7 +464,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Parse parameter value", + "name": "input1" + } + ], "label": "Estimated genome size", "name": "Parse parameter value", "outputs": [ @@ -495,7 +520,16 @@ "output_name": "split_fasta" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Map with minimap2", + "name": "fastq_input" + }, + { + "description": "runtime parameter for tool Map with minimap2", + "name": "reference_source" + } + ], "label": null, "name": "Map with minimap2", "outputs": [ @@ -542,7 +576,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cut", + "name": "input" + } + ], "label": null, "name": "Cut", "outputs": [ @@ -575,7 +614,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cut", + "name": "input" + } + ], "label": null, "name": "Cut", "outputs": [ @@ -608,7 +652,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Parse parameter value", + "name": "input1" + } + ], "label": null, "name": "Parse parameter value", "outputs": [ @@ -668,7 +717,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Parse parameter value", + "name": "input1" + } + ], "label": null, "name": "Parse parameter value", "outputs": [ @@ -715,7 +769,12 @@ "output_name": "integer_param" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + } + ], "label": null, "name": "Purge overlaps", "outputs": [ @@ -836,7 +895,20 @@ "output_name": "alignment_output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + }, + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + }, + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + } + ], "label": null, "name": "Purge overlaps", "outputs": [ @@ -898,7 +970,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + }, + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + } + ], "label": null, "name": "Purge overlaps", "outputs": [ @@ -980,7 +1061,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Concatenate datasets", + "name": "input1" + } + ], "label": null, "name": "Concatenate datasets", "outputs": [ @@ -1030,7 +1116,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Busco", + "name": "input" + }, + { + "description": "runtime parameter for tool Busco", + "name": "lineage" + } + ], "label": null, "name": "Busco", "outputs": [ @@ -1125,7 +1220,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "input_file" + }, + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1182,7 +1286,12 @@ "output_name": "integer_param" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "input_file" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1229,7 +1338,12 @@ "output_name": "get_seqs_purged" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "input_file" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1280,7 +1394,16 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Map with minimap2", + "name": "fastq_input" + }, + { + "description": "runtime parameter for tool Map with minimap2", + "name": "reference_source" + } + ], "label": null, "name": "Map with minimap2", "outputs": [ @@ -1334,7 +1457,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + } + ], "label": null, "name": "Purge overlaps", "outputs": [ @@ -1386,7 +1514,12 @@ "output_name": "stats" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Text reformatting", + "name": "infile" + } + ], "label": null, "name": "Text reformatting", "outputs": [ @@ -1408,7 +1541,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", "tool_shed_repository": { - "changeset_revision": "d698c222f354", + "changeset_revision": "ddf54b12c295", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1441,6 +1574,7 @@ "subworkflow": { "a_galaxy_workflow": "true", "annotation": "", + "comments": [], "format-version": "0.1", "name": "gfastats_data_prep", "steps": { @@ -1482,7 +1616,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Sort", + "name": "input" + } + ], "label": null, "name": "Sort", "outputs": [ @@ -1521,7 +1660,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Text reformatting", + "name": "infile" + } + ], "label": null, "name": "Text reformatting", "outputs": [ @@ -1543,7 +1687,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", "tool_shed_repository": { - "changeset_revision": "d698c222f354", + "changeset_revision": "ddf54b12c295", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1566,7 +1710,12 @@ "output_name": "outfile" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Datamash", + "name": "in_file" + } + ], "label": null, "name": "Datamash", "outputs": [ @@ -1611,7 +1760,12 @@ "output_name": "outfile" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Add column", + "name": "input" + } + ], "label": null, "name": "Add column", "outputs": [ @@ -1656,7 +1810,12 @@ "output_name": "out_file" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Parse parameter value", + "name": "input1" + } + ], "label": null, "name": "Parse parameter value", "outputs": [ @@ -1744,7 +1903,12 @@ "output_name": "out1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Compute", + "name": "input" + } + ], "label": null, "name": "Compute", "outputs": [ @@ -1815,7 +1979,12 @@ "output_name": "integer_param" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + } + ], "label": null, "name": "Purge overlaps", "outputs": [ @@ -1939,7 +2108,16 @@ "output_name": "split_fasta" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Map with minimap2", + "name": "fastq_input" + }, + { + "description": "runtime parameter for tool Map with minimap2", + "name": "reference_source" + } + ], "label": null, "name": "Map with minimap2", "outputs": [ @@ -2001,7 +2179,20 @@ "output_name": "alignment_output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + }, + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + }, + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + } + ], "label": null, "name": "Purge overlaps", "outputs": [ @@ -2063,7 +2254,16 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + }, + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + } + ], "label": null, "name": "Purge overlaps", "outputs": [ @@ -2138,7 +2338,12 @@ "output_name": "integer_param" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "input_file" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -2185,7 +2390,12 @@ "output_name": "get_seqs_purged" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "input_file" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -2240,7 +2450,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Merqury", + "name": "mode" + } + ], "label": null, "name": "Merqury", "outputs": [ @@ -2256,6 +2471,10 @@ "name": "stats_files", "type": "input" }, + { + "name": "hist_files", + "type": "input" + }, { "name": "log_file", "type": "txt" @@ -2321,7 +2540,7 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"label\": \"output_merqury\", \"mode\": {\"options\": \"default\", \"__current_case__\": 0, \"meryldb_F1\": {\"__class__\": \"ConnectedValue\"}, \"assembly_options\": {\"number_assemblies\": \"two\", \"__current_case__\": 1, \"assembly_01\": {\"__class__\": \"ConnectedValue\"}, \"assembly_02\": {\"__class__\": \"ConnectedValue\"}}}, \"output_add_headers\": false, \"output_selector\": [\"qv\", \"plots\", \"stats\", \"log\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"label\": \"output_merqury\", \"mode\": {\"options\": \"default\", \"__current_case__\": 0, \"meryldb_F1\": {\"__class__\": \"RuntimeValue\"}, \"assembly_options\": {\"number_assemblies\": \"two\", \"__current_case__\": 1, \"assembly_01\": {\"__class__\": \"RuntimeValue\"}, \"assembly_02\": {\"__class__\": \"RuntimeValue\"}}}, \"output_add_headers\": false, \"output_selector\": [\"qv\", \"plots\", \"stats\", \"log\", \"hist\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.3+galaxy3", "type": "tool", "uuid": "133c60bc-4171-44b4-bf22-c70c623265b2", @@ -2354,7 +2573,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "input_file" + }, + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -2407,7 +2635,12 @@ "output_name": "stats" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Text reformatting", + "name": "infile" + } + ], "label": null, "name": "Text reformatting", "outputs": [ @@ -2429,7 +2662,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", "tool_shed_repository": { - "changeset_revision": "d698c222f354", + "changeset_revision": "ddf54b12c295", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -2462,6 +2695,7 @@ "subworkflow": { "a_galaxy_workflow": "true", "annotation": "", + "comments": [], "format-version": "0.1", "name": "gfastats_data_prep", "steps": { @@ -2503,7 +2737,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Sort", + "name": "input" + } + ], "label": null, "name": "Sort", "outputs": [ @@ -2542,7 +2781,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Text reformatting", + "name": "infile" + } + ], "label": null, "name": "Text reformatting", "outputs": [ @@ -2564,7 +2808,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", "tool_shed_repository": { - "changeset_revision": "d698c222f354", + "changeset_revision": "ddf54b12c295", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -2587,7 +2831,12 @@ "output_name": "outfile" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Datamash", + "name": "in_file" + } + ], "label": null, "name": "Datamash", "outputs": [ @@ -2632,7 +2881,12 @@ "output_name": "outfile" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Add column", + "name": "input" + } + ], "label": null, "name": "Add column", "outputs": [ @@ -2677,7 +2931,12 @@ "output_name": "out_file" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Parse parameter value", + "name": "input1" + } + ], "label": null, "name": "Parse parameter value", "outputs": [ @@ -2765,7 +3024,12 @@ "output_name": "out1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Compute", + "name": "input" + } + ], "label": null, "name": "Compute", "outputs": [ @@ -2832,7 +3096,16 @@ "output_name": "outfile" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Join", + "name": "infile1" + }, + { + "description": "runtime parameter for tool Join", + "name": "infile2" + } + ], "label": null, "name": "Join", "outputs": [ @@ -2856,7 +3129,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2", "tool_shed_repository": { - "changeset_revision": "d698c222f354", + "changeset_revision": "ddf54b12c295", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -2910,6 +3183,7 @@ "subworkflow": { "a_galaxy_workflow": "true", "annotation": "", + "comments": [], "creator": [ { "class": "Organization", @@ -3060,7 +3334,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Add column", + "name": "exp" + }, + { + "description": "runtime parameter for tool Add column", + "name": "input" + } + ], "label": null, "name": "Add column", "outputs": [ @@ -3109,7 +3392,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Add column", + "name": "exp" + }, + { + "description": "runtime parameter for tool Add column", + "name": "input" + } + ], "label": null, "name": "Add column", "outputs": [ @@ -3158,7 +3450,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Concatenate datasets", + "name": "inputs" + } + ], "label": null, "name": "Concatenate datasets", "outputs": [ @@ -3203,7 +3500,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cut", + "name": "input" + } + ], "label": null, "name": "Cut", "outputs": [ @@ -3242,7 +3544,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cut", + "name": "input" + } + ], "label": null, "name": "Cut", "outputs": [ @@ -3281,7 +3588,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Scatterplot with ggplot2", + "name": "input1" + } + ], "label": "Nx Plot", "name": "Scatterplot with ggplot2", "outputs": [ @@ -3341,7 +3653,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Scatterplot with ggplot2", + "name": "input1" + } + ], "label": "Size Plot", "name": "Scatterplot with ggplot2", "outputs": [ @@ -3415,6 +3732,6 @@ "tags": [ "VGP_curated" ], - "uuid": "a6c2fa10-d553-47a1-813f-12173d435709", - "version": 4 + "uuid": "6b1b52f2-833c-4532-95c0-c85bc238fc76", + "version": 1 } \ No newline at end of file