diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml index 68205c04a..6c3117206 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml @@ -32,6 +32,7 @@ Name for Haplotype 1: Hap1 Name for Haplotype 2: Hap2 Homozygous Read Coverage: null + Database for Busco Lineage: v5 outputs: Hifiasm HiC hap1: assert: diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga index 46254fdae..0c1e60942 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga @@ -20,7 +20,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.2.1", + "release": "0.2.2", "name": "Assembly-Hifi-HiC-phasing-VGP4", "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\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" @@ -162,11 +162,44 @@ "workflow_outputs": [] }, "5": { - "annotation": "Taxonomic lineage for the organism being assembled for Busco analysis", + "annotation": "", "content_id": null, "errors": null, "id": 5, "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Database for Busco Lineage" + } + ], + "label": "Database for Busco Lineage", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 81.55189123074645, + "top": 666.080035105452 + }, + "tool_id": null, + "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "245a5b51-c40d-4425-81ca-2baf3c157022", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "07c8cb5a-ff7f-4e51-8f81-74b2f7630f2e" + } + ] + }, + "6": { + "annotation": "Taxonomic lineage for the organism being assembled for Busco analysis", + "content_id": null, + "errors": null, + "id": 6, + "input_connections": {}, "inputs": [ { "description": "Taxonomic lineage for the organism being assembled for Busco analysis", @@ -177,8 +210,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 48.90625, - "top": 607.51953125 + "left": 112.31427690494708, + "top": 770.3740188995779 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", @@ -186,13 +219,19 @@ "type": "parameter_input", "uuid": "a9df063c-37ef-440d-93e6-212ac3a598e8", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "4c2b1889-3936-4df2-8375-250ca7dea2c7" + } + ] }, - "6": { + "7": { "annotation": "", "content_id": null, "errors": null, - "id": 6, + "id": 7, "input_connections": {}, "inputs": [ { @@ -204,8 +243,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 66.703125, - "top": 671.3125 + "left": 122.01184397539753, + "top": 852.6092753452594 }, "tool_id": null, "tool_state": "{\"default\": \"Hap1\", \"parameter_type\": \"text\", \"optional\": true}", @@ -213,13 +252,19 @@ "type": "parameter_input", "uuid": "41d1bb31-75f9-4034-abad-96aed4916b45", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "34ed45e3-2132-4c67-af2a-b72a8cbcf55c" + } + ] }, - "7": { + "8": { "annotation": "", "content_id": null, "errors": null, - "id": 7, + "id": 8, "input_connections": {}, "inputs": [ { @@ -231,8 +276,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 78.38870701261258, - "top": 769.8272396352553 + "left": 130.80851045942487, + "top": 939.8716854194543 }, "tool_id": null, "tool_state": "{\"default\": \"Hap2\", \"parameter_type\": \"text\", \"optional\": true}", @@ -240,13 +285,19 @@ "type": "parameter_input", "uuid": "6d5afa06-c3e8-4eb7-8819-8cfe8300c462", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "8c9ba587-c3e2-4200-8794-2b18ba08fc9e" + } + ] }, - "8": { + "9": { "annotation": "Defaults to 37 if not specified. For genomes much larger than human, applying -f38 or even -f39 is preferred to save memory on k-mer counting.", "content_id": null, "errors": null, - "id": 8, + "id": 9, "input_connections": {}, "inputs": [ { @@ -258,8 +309,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 96.0148601509567, - "top": 866.2253241049863 + "left": 137.2665356894154, + "top": 1033.0113085913417 }, "tool_id": null, "tool_state": "{\"default\": 37, \"parameter_type\": \"integer\", \"optional\": true}", @@ -267,13 +318,19 @@ "type": "parameter_input", "uuid": "b949921b-95a3-4d43-81b2-4006a4909e4b", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "0696f3a8-cd87-4b44-a71c-54611b53be34" + } + ] }, - "9": { + "10": { "annotation": "", "content_id": null, "errors": null, - "id": 9, + "id": 10, "input_connections": {}, "inputs": [ { @@ -285,8 +342,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 105.51087786212338, - "top": 966.1883445504246 + "left": 145.73965411666467, + "top": 1117.6864372730274 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": \"\"}", @@ -294,13 +351,19 @@ "type": "data_input", "uuid": "557a2e2b-008c-4566-836a-6509950aa85b", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "7b3c62fb-1823-4366-92b7-053ea9054620" + } + ] }, - "10": { + "11": { "annotation": "If empty, read coverage will be estimated from the Genomescope parameters. ", "content_id": null, "errors": null, - "id": 10, + "id": 11, "input_connections": {}, "inputs": [ { @@ -321,13 +384,19 @@ "type": "parameter_input", "uuid": "b251eddc-49e6-4899-a893-a904c29b9e75", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "2e143429-f516-4a3d-8983-08df349be75f" + } + ] }, - "11": { + "12": { "annotation": "GenomeScope model parameters generated by K-mer profiling workflow", "content_id": null, "errors": null, - "id": 11, + "id": 12, "input_connections": {}, "inputs": [ { @@ -350,11 +419,11 @@ "when": null, "workflow_outputs": [] }, - "12": { + "13": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "errors": null, - "id": 12, + "id": 13, "input_connections": { "library|input_1": { "id": 0, @@ -428,11 +497,11 @@ } ] }, - "13": { + "14": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1", "errors": null, - "id": 13, + "id": 14, "input_connections": { "infile": { "id": 3, @@ -473,14 +542,14 @@ "when": null, "workflow_outputs": [] }, - "14": { + "15": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0", "errors": null, - "id": 14, + "id": 15, "input_connections": { "input": { - "id": 11, + "id": 12, "output_name": "output" } }, @@ -518,14 +587,14 @@ "when": null, "workflow_outputs": [] }, - "15": { + "16": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", "errors": null, - "id": 15, + "id": 16, "input_connections": { "results_0|software_cond|input": { - "id": 12, + "id": 13, "output_name": "report" } }, @@ -561,14 +630,14 @@ "when": null, "workflow_outputs": [] }, - "16": { + "17": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "errors": null, - "id": 16, + "id": 17, "input_connections": { "infile": { - "id": 13, + "id": 14, "output_name": "output" } }, @@ -606,14 +675,14 @@ "when": null, "workflow_outputs": [] }, - "17": { + "18": { "annotation": "", "content_id": "Cut1", "errors": null, - "id": 17, + "id": 18, "input_connections": { "input": { - "id": 14, + "id": 15, "output_name": "out_file1" } }, @@ -645,14 +714,14 @@ "when": null, "workflow_outputs": [] }, - "18": { + "19": { "annotation": "", "content_id": "Convert characters1", "errors": null, - "id": 18, + "id": 19, "input_connections": { "input": { - "id": 16, + "id": 17, "output_name": "outfile" } }, @@ -684,14 +753,14 @@ "when": null, "workflow_outputs": [] }, - "19": { + "20": { "annotation": "", "content_id": "param_value_from_file", "errors": null, - "id": 19, + "id": 20, "input_connections": { "input1": { - "id": 17, + "id": 18, "output_name": "out_file1" } }, @@ -730,14 +799,14 @@ "when": null, "workflow_outputs": [] }, - "20": { + "21": { "annotation": "", "content_id": "Cut1", "errors": null, - "id": 20, + "id": 21, "input_connections": { "input": { - "id": 18, + "id": 19, "output_name": "out_file1" } }, @@ -769,18 +838,18 @@ "when": null, "workflow_outputs": [] }, - "21": { + "22": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, - "id": 21, + "id": 22, "input_connections": { "style_cond|type_cond|pick_from_0|value": { - "id": 10, + "id": 11, "output_name": "output" }, "style_cond|type_cond|pick_from_1|value": { - "id": 19, + "id": 20, "output_name": "integer_param" } }, @@ -820,14 +889,14 @@ "when": null, "workflow_outputs": [] }, - "22": { + "23": { "annotation": "", "content_id": "param_value_from_file", "errors": null, - "id": 22, + "id": 23, "input_connections": { "input1": { - "id": 20, + "id": 21, "output_name": "out_file1" } }, @@ -874,18 +943,18 @@ } ] }, - "23": { + "24": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0", "errors": null, - "id": 23, + "id": 24, "input_connections": { "assembly_options|hom_cov": { - "id": 21, + "id": 22, "output_name": "integer_param" }, "filter_bits": { - "id": 8, + "id": 9, "output_name": "output" }, "hic_partition|h1": { @@ -897,7 +966,7 @@ "output_name": "output" }, "mode|reads": { - "id": 12, + "id": 13, "output_name": "out1" } }, @@ -999,14 +1068,14 @@ "when": null, "workflow_outputs": [] }, - "24": { + "25": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4", "errors": null, - "id": 24, + "id": 25, "input_connections": { "input_file": { - "id": 23, + "id": 24, "output_name": "hic_raw_initig" } }, @@ -1052,18 +1121,18 @@ } ] }, - "25": { + "26": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 25, + "id": 26, "input_connections": { "input_file": { - "id": 23, + "id": 24, "output_name": "hic_balanced_contig_hap2_graph" }, "mode_condition|statistics_condition|expected_genomesize": { - "id": 22, + "id": 23, "output_name": "integer_param" } }, @@ -1110,18 +1179,18 @@ "when": null, "workflow_outputs": [] }, - "26": { + "27": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 26, + "id": 27, "input_connections": { "input_file": { - "id": 23, + "id": 24, "output_name": "hic_balanced_contig_hap1_graph" }, "mode_condition|statistics_condition|expected_genomesize": { - "id": 22, + "id": 23, "output_name": "integer_param" } }, @@ -1168,14 +1237,14 @@ "when": null, "workflow_outputs": [] }, - "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": 23, + "id": 24, "output_name": "hic_balanced_contig_hap2_graph" } }, @@ -1222,14 +1291,14 @@ "when": null, "workflow_outputs": [] }, - "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": 23, + "id": 24, "output_name": "hic_balanced_contig_hap2_graph" } }, @@ -1282,14 +1351,14 @@ } ] }, - "29": { + "30": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 29, + "id": 30, "input_connections": { "input_file": { - "id": 23, + "id": 24, "output_name": "hic_balanced_contig_hap1_graph" } }, @@ -1336,14 +1405,14 @@ "when": null, "workflow_outputs": [] }, - "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": 23, + "id": 24, "output_name": "hic_balanced_contig_hap1_graph" } }, @@ -1396,18 +1465,18 @@ } ] }, - "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": 23, + "id": 24, "output_name": "hic_balanced_contig_hap2_graph" }, "mode_condition|swiss_army_knife": { - "id": 9, + "id": 10, "output_name": "output" } }, @@ -1445,18 +1514,18 @@ "when": null, "workflow_outputs": [] }, - "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": 23, + "id": 24, "output_name": "hic_balanced_contig_hap1_graph" }, "mode_condition|swiss_army_knife": { - "id": 9, + "id": 10, "output_name": "output" } }, @@ -1494,14 +1563,14 @@ "when": null, "workflow_outputs": [] }, - "33": { + "34": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "errors": null, - "id": 33, + "id": 34, "input_connections": { "infile": { - "id": 25, + "id": 26, "output_name": "stats" } }, @@ -1539,14 +1608,14 @@ "when": null, "workflow_outputs": [] }, - "34": { + "35": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "errors": null, - "id": 34, + "id": 35, "input_connections": { "infile": { - "id": 26, + "id": 27, "output_name": "stats" } }, @@ -1584,12 +1653,12 @@ "when": null, "workflow_outputs": [] }, - "35": { + "36": { "annotation": "", - "id": 35, + "id": 36, "input_connections": { "gfa_stats": { - "id": 27, + "id": 28, "input_subworkflow_step_id": 0, "output_name": "stats" } @@ -1966,12 +2035,12 @@ "when": null, "workflow_outputs": [] }, - "36": { + "37": { "annotation": "", - "id": 36, + "id": 37, "input_connections": { "gfa_stats": { - "id": 29, + "id": 30, "input_subworkflow_step_id": 0, "output_name": "stats" } @@ -2348,14 +2417,14 @@ "when": null, "workflow_outputs": [] }, - "37": { + "38": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1", "errors": null, - "id": 37, + "id": 38, "input_connections": { "infile": { - "id": 31, + "id": 32, "output_name": "output" } }, @@ -2408,14 +2477,14 @@ } ] }, - "38": { + "39": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1", "errors": null, - "id": 38, + "id": 39, "input_connections": { "infile": { - "id": 32, + "id": 33, "output_name": "output" } }, @@ -2468,18 +2537,18 @@ } ] }, - "39": { + "40": { "annotation": "", "content_id": "join1", "errors": null, - "id": 39, + "id": 40, "input_connections": { "input1": { - "id": 34, + "id": 35, "output_name": "outfile" }, "input2": { - "id": 33, + "id": 34, "output_name": "outfile" } }, @@ -2511,27 +2580,27 @@ "when": null, "workflow_outputs": [] }, - "40": { + "41": { "annotation": "", - "id": 40, + "id": 41, "input_connections": { "Alternate data": { - "id": 35, + "id": 36, "input_subworkflow_step_id": 1, "output_name": "gfastats data for plotting" }, "Name of alternate assembly": { - "id": 7, + "id": 8, "input_subworkflow_step_id": 3, "output_name": "output" }, "Name of primary assembly": { - "id": 6, + "id": 7, "input_subworkflow_step_id": 2, "output_name": "output" }, "Primary data": { - "id": 36, + "id": 37, "input_subworkflow_step_id": 0, "output_name": "gfastats data for plotting" } @@ -3054,19 +3123,23 @@ } ] }, - "41": { + "42": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0", "errors": null, - "id": 41, + "id": 42, "input_connections": { "input": { - "id": 37, + "id": 38, "output_name": "output" }, - "lineage|lineage_dataset": { + "lineage_conditional|cached_db": { "id": 5, "output_name": "output" + }, + "lineage|lineage_dataset": { + "id": 6, + "output_name": "output" } }, "inputs": [], @@ -3142,16 +3215,16 @@ "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__\": \"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\", \"gff\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "5.5.0+galaxy0", "type": "tool", "uuid": "08066bc3-0992-4606-844d-16be3c56691a", "when": null, "workflow_outputs": [ { - "label": "Busco Summary Image Hap2", - "output_name": "summary_image", - "uuid": "84725fc4-3480-44a2-abc0-abc8f54addb1" + "label": "Busco Gff File - Hap2", + "output_name": "busco_gff", + "uuid": "3b8e8b67-ad7d-4d30-a253-e601d3e201d2" }, { "label": "Busco Summary Hap2", @@ -3159,24 +3232,24 @@ "uuid": "bf7e959c-5252-467e-bb58-2b8cabbd0f3b" }, { - "label": "Busco Gff File - Hap2", - "output_name": "busco_gff", - "uuid": "3b8e8b67-ad7d-4d30-a253-e601d3e201d2" + "label": "Busco Summary Image Hap2", + "output_name": "summary_image", + "uuid": "84725fc4-3480-44a2-abc0-abc8f54addb1" } ] }, - "42": { + "43": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4", "errors": null, - "id": 42, + "id": 43, "input_connections": { "mode|assembly_options|assembly_01": { - "id": 38, + "id": 39, "output_name": "output" }, "mode|assembly_options|assembly_02": { - "id": 37, + "id": 38, "output_name": "output" }, "mode|meryldb_F1": { @@ -3282,6 +3355,11 @@ "uuid": "9985e575-3113-4c2c-bc2c-78faab3a1291", "when": null, "workflow_outputs": [ + { + "label": "Merqury Stats", + "output_name": "stats_files", + "uuid": "22a82fae-74cf-4024-9815-ba6a9892aac3" + }, { "label": "Merqury images", "output_name": "png_files", @@ -3296,27 +3374,26 @@ "label": "Merqury QV", "output_name": "qv_files", "uuid": "5ba07c29-6ca5-42bd-a1e8-f4f6a35c3814" - }, - { - "label": "Merqury Stats", - "output_name": "stats_files", - "uuid": "22a82fae-74cf-4024-9815-ba6a9892aac3" } ] }, - "43": { + "44": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0", "errors": null, - "id": 43, + "id": 44, "input_connections": { "input": { - "id": 38, + "id": 39, "output_name": "output" }, - "lineage|lineage_dataset": { + "lineage_conditional|cached_db": { "id": 5, "output_name": "output" + }, + "lineage|lineage_dataset": { + "id": 6, + "output_name": "output" } }, "inputs": [], @@ -3345,8 +3422,8 @@ } ], "position": { - "left": 2568.723853333207, - "top": 1078.3517946538443 + "left": 2599.0485857103813, + "top": 1053.6223175775656 }, "post_job_actions": { "TagDatasetActionbusco_gff": { @@ -3392,16 +3469,16 @@ "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__\": \"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\", \"gff\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "5.5.0+galaxy0", "type": "tool", "uuid": "a4957dee-45cc-4f34-ae2e-e07f93b9fcc4", "when": null, "workflow_outputs": [ { - "label": "Busco Summary Image Hap1", - "output_name": "summary_image", - "uuid": "cfac3083-4c1e-4bb4-91a5-eba5d19f2757" + "label": "Busco Summary Hap1", + "output_name": "busco_sum", + "uuid": "bd6443ea-5266-4dfc-8f1e-aded27317da8" }, { "label": "Busco Gff File - Hap1", @@ -3409,20 +3486,20 @@ "uuid": "ba26cb24-25d4-4669-982c-abe4816753a6" }, { - "label": "Busco Summary Hap1", - "output_name": "busco_sum", - "uuid": "bd6443ea-5266-4dfc-8f1e-aded27317da8" + "label": "Busco Summary Image Hap1", + "output_name": "summary_image", + "uuid": "cfac3083-4c1e-4bb4-91a5-eba5d19f2757" } ] }, - "44": { + "45": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1", "errors": null, - "id": 44, + "id": 45, "input_connections": { "input": { - "id": 39, + "id": 40, "output_name": "out_file1" } }, @@ -3475,14 +3552,14 @@ } ] }, - "45": { + "46": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 45, + "id": 46, "input_connections": { "input": { - "id": 42, + "id": 43, "output_name": "png_files" } }, @@ -3520,14 +3597,14 @@ } ] }, - "46": { + "47": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 46, + "id": 47, "input_connections": { "input": { - "id": 42, + "id": 43, "output_name": "png_files" } }, @@ -3565,14 +3642,14 @@ } ] }, - "47": { + "48": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 47, + "id": 48, "input_connections": { "input": { - "id": 42, + "id": 43, "output_name": "qv_files" } }, @@ -3610,14 +3687,14 @@ } ] }, - "48": { + "49": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 48, + "id": 49, "input_connections": { "input": { - "id": 42, + "id": 43, "output_name": "png_files" } }, @@ -3655,14 +3732,14 @@ } ] }, - "49": { + "50": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 49, + "id": 50, "input_connections": { "input": { - "id": 42, + "id": 43, "output_name": "stats_files" } }, @@ -3700,14 +3777,14 @@ } ] }, - "50": { + "51": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, - "id": 50, + "id": 51, "input_connections": { "input": { - "id": 42, + "id": 43, "output_name": "png_files" } }, @@ -3745,14 +3822,14 @@ } ] }, - "51": { + "52": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "errors": null, - "id": 51, + "id": 52, "input_connections": { "infile": { - "id": 44, + "id": 45, "output_name": "output" } }, @@ -3801,6 +3878,6 @@ "VGP", "Reviewed" ], - "uuid": "4135d455-ac66-4d86-b4a3-643580ff877f", - "version": 5 -} + "uuid": "cb0e2983-13df-451c-85a2-ee78c94a2bd2", + "version": 1 +} \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md index 06dad0676..048600877 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md @@ -1,5 +1,9 @@ # Changelog +## [0.2.2] 2024-08-07 + +- Expose parameter: Busco lineage database + ## [0.2.1] 2024-07-29 ### Automatic update