From a5f26409b28f358093b130e3ab2a25aa43dd2042 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 14 Oct 2024 04:22:14 +0000 Subject: [PATCH 1/6] Updating workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3 from 0.2.1 to 0.2.2 --- .../Assembly-Hifi-only-VGP3.ga | 224 +++++++++++------- .../Assembly-Hifi-only-VGP3/CHANGELOG.md | 9 + 2 files changed, 145 insertions(+), 88 deletions(-) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga index 136b94576..31867824e 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga @@ -15,7 +15,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.2.1", + "release": "0.2.2", "name": "Assembly-Hifi-only-VGP3", "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\n\n## BUSCO results (Vertebrata database)\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" @@ -329,7 +329,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cutadapt", + "name": "library" + } + ], "label": null, "name": "Cutadapt", "outputs": [ @@ -411,7 +416,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -464,7 +469,7 @@ }, "14": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", "errors": null, "id": 14, "input_connections": { @@ -493,15 +498,15 @@ "output_name": "out_file1" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", "tool_shed_repository": { - "changeset_revision": "6595517c2dd8", + "changeset_revision": "aff5135563c6", "name": "column_maker", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"c3*2\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.0", + "tool_version": "2.1", "type": "tool", "uuid": "0203b86a-9457-48fc-87af-e251b24bad2b", "when": null, @@ -509,7 +514,7 @@ }, "15": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "errors": null, "id": 15, "input_connections": { @@ -522,13 +527,13 @@ "label": null, "name": "MultiQC", "outputs": [ - { - "name": "stats", - "type": "input" - }, { "name": "html_report", "type": "html" + }, + { + "name": "stats", + "type": "tabular" } ], "position": { @@ -536,15 +541,15 @@ "top": 1052.86328125 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "abfd8a6544d7", + "changeset_revision": "f7e2f1eb3a16", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.11+galaxy1", + "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "24ef7e9a-d7eb-4cda-8675-26e8ea167b54", "when": null, @@ -594,7 +599,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -888,7 +893,16 @@ "output_name": "out1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Hifiasm", + "name": "assembly_options" + }, + { + "description": "runtime parameter for tool Hifiasm", + "name": "mode" + } + ], "label": null, "name": "Hifiasm", "outputs": [ @@ -1038,7 +1052,7 @@ }, "25": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0", "errors": null, "id": 25, "input_connections": { @@ -1051,7 +1065,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1080,15 +1099,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0", "tool_shed_repository": { - "changeset_revision": "3ef480892a9f", + "changeset_revision": "6ec1b853c8fd", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"no\", \"__current_case__\": 0}}, \"discover_paths\": true, \"sort\": \"\", \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.6+galaxy0", + "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"no\", \"__current_case__\": 0}}, \"discover_paths\": true, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.3.8+galaxy0", "type": "tool", "uuid": "18417334-ada9-4ac4-bc1f-9707f3200dfa", "when": null, @@ -1102,7 +1121,7 @@ }, "26": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0", "errors": null, "id": 26, "input_connections": { @@ -1115,7 +1134,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1144,15 +1168,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0", "tool_shed_repository": { - "changeset_revision": "3ef480892a9f", + "changeset_revision": "6ec1b853c8fd", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"no\", \"__current_case__\": 0}}, \"discover_paths\": true, \"sort\": \"\", \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.6+galaxy0", + "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"no\", \"__current_case__\": 0}}, \"discover_paths\": true, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.3.8+galaxy0", "type": "tool", "uuid": "2dcb95b0-743f-4855-8a3c-d17e9d0656e7", "when": null, @@ -1166,7 +1190,7 @@ }, "27": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0", "errors": null, "id": 27, "input_connections": { @@ -1179,7 +1203,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1215,15 +1244,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0", "tool_shed_repository": { - "changeset_revision": "3ef480892a9f", + "changeset_revision": "6ec1b853c8fd", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"fasta\", \"__current_case__\": 0, \"line_length\": null}, \"discover_paths\": true, \"sort\": \"\", \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.6+galaxy0", + "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"fasta\", \"__current_case__\": 0, \"line_length\": null}, \"discover_paths\": true, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.3.8+galaxy0", "type": "tool", "uuid": "ebb8800f-c58b-4118-93a3-a417631919db", "when": null, @@ -1237,7 +1266,7 @@ }, "28": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0", "errors": null, "id": 28, "input_connections": { @@ -1250,7 +1279,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -1286,15 +1320,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0", "tool_shed_repository": { - "changeset_revision": "3ef480892a9f", + "changeset_revision": "6ec1b853c8fd", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"fasta\", \"__current_case__\": 0, \"line_length\": null}, \"discover_paths\": true, \"sort\": \"\", \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.6+galaxy0", + "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"fasta\", \"__current_case__\": 0, \"line_length\": null}, \"discover_paths\": true, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.3.8+galaxy0", "type": "tool", "uuid": "c6bd9a9c-c058-47dc-85cb-d5ba5e38490a", "when": null, @@ -1308,7 +1342,7 @@ }, "29": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0", "errors": null, "id": 29, "input_connections": { @@ -1343,15 +1377,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0", "tool_shed_repository": { - "changeset_revision": "3ef480892a9f", + "changeset_revision": "6ec1b853c8fd", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"assembly\", \"__current_case__\": 2, \"expected_genomesize\": {\"__class__\": \"ConnectedValue\"}}, \"locale\": true, \"tabular\": true, \"discover_paths\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.6+galaxy0", + "tool_version": "1.3.8+galaxy0", "type": "tool", "uuid": "29d8eb08-28d9-4b2a-b61c-fcfbe634d4e9", "when": null, @@ -1365,7 +1399,7 @@ }, "30": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0", "errors": null, "id": 30, "input_connections": { @@ -1400,15 +1434,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0", "tool_shed_repository": { - "changeset_revision": "3ef480892a9f", + "changeset_revision": "6ec1b853c8fd", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"assembly\", \"__current_case__\": 2, \"expected_genomesize\": {\"__class__\": \"ConnectedValue\"}}, \"locale\": true, \"tabular\": true, \"discover_paths\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.6+galaxy0", + "tool_version": "1.3.8+galaxy0", "type": "tool", "uuid": "6b62822f-2c9f-41d6-acdd-45e13c52b1fb", "when": null, @@ -1422,7 +1456,7 @@ }, "31": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0", "errors": null, "id": 31, "input_connections": { @@ -1458,15 +1492,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0", "tool_shed_repository": { - "changeset_revision": "3ef480892a9f", + "changeset_revision": "6ec1b853c8fd", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"size\", \"__current_case__\": 0, \"out_size\": \"c\"}, \"locale\": false, \"tabular\": true, \"discover_paths\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.6+galaxy0", + "tool_version": "1.3.8+galaxy0", "type": "tool", "uuid": "0e65f363-c145-4b0e-987e-9a13e822dbdf", "when": null, @@ -1474,7 +1508,7 @@ }, "32": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0", "errors": null, "id": 32, "input_connections": { @@ -1510,15 +1544,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0", "tool_shed_repository": { - "changeset_revision": "3ef480892a9f", + "changeset_revision": "6ec1b853c8fd", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"size\", \"__current_case__\": 0, \"out_size\": \"c\"}, \"locale\": false, \"tabular\": true, \"discover_paths\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.6+galaxy0", + "tool_version": "1.3.8+galaxy0", "type": "tool", "uuid": "70b12ad8-64c9-401c-a50d-69178b9e7321", "when": null, @@ -1526,7 +1560,7 @@ }, "33": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0", "errors": null, "id": 33, "input_connections": { @@ -1543,7 +1577,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Busco", + "name": "lineage" + }, + { + "description": "runtime parameter for tool Busco", + "name": "lineage_conditional" + } + ], "label": null, "name": "Busco", "outputs": [ @@ -1609,15 +1652,15 @@ "output_name": "summary_image" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "ea8146ee148f", + "changeset_revision": "2babe6d5c561", "name": "busco", "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__\": \"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", + "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"miniprot\", \"__current_case__\": 1}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"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": "5.7.1+galaxy0", "type": "tool", "uuid": "1cd23635-275c-411f-b91d-f53f2bb229cb", "when": null, @@ -1648,7 +1691,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Merqury", + "name": "mode" + } + ], "label": null, "name": "Merqury", "outputs": [ @@ -1796,7 +1844,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1841,7 +1889,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1982,7 +2030,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -2170,7 +2218,7 @@ }, "7": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", "errors": null, "id": 7, "input_connections": { @@ -2205,15 +2253,15 @@ "output_name": "out_file1" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", "tool_shed_repository": { - "changeset_revision": "6595517c2dd8", + "changeset_revision": "aff5135563c6", "name": "column_maker", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": {\"__class__\": \"ConnectedValue\"}, \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}, {\"__index__\": 1, \"cond\": \"c2/1000000\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}, {\"__index__\": 2, \"cond\": \"c3/1000000\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.0", + "tool_version": "2.1", "type": "tool", "uuid": "c93568ca-103f-4d8e-af88-d6de721e30cd", "when": null, @@ -2227,7 +2275,7 @@ } }, "tags": [], - "uuid": "dd05abfc-037d-43f6-8f1e-08e9aaa2e4e0" + "uuid": "8e50f47e-494e-44ae-af08-e31da30a873e" }, "tool_id": null, "type": "subworkflow", @@ -2364,7 +2412,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -2552,7 +2600,7 @@ }, "7": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", "errors": null, "id": 7, "input_connections": { @@ -2587,15 +2635,15 @@ "output_name": "out_file1" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", "tool_shed_repository": { - "changeset_revision": "6595517c2dd8", + "changeset_revision": "aff5135563c6", "name": "column_maker", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": {\"__class__\": \"ConnectedValue\"}, \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}, {\"__index__\": 1, \"cond\": \"c2/1000000\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}, {\"__index__\": 2, \"cond\": \"c3/1000000\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.0", + "tool_version": "2.1", "type": "tool", "uuid": "c93568ca-103f-4d8e-af88-d6de721e30cd", "when": null, @@ -2609,7 +2657,7 @@ } }, "tags": [], - "uuid": "49338064-96ab-4998-9857-63df8cdc04a8" + "uuid": "f888dd45-2f79-45f9-83d6-dbe483be29a3" }, "tool_id": null, "type": "subworkflow", @@ -3191,7 +3239,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -3323,7 +3371,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1", "tool_shed_repository": { - "changeset_revision": "3b12bf9b4b87", + "changeset_revision": "5298e06f14f9", "name": "ggplot2_point", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -3383,7 +3431,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1", "tool_shed_repository": { - "changeset_revision": "3b12bf9b4b87", + "changeset_revision": "5298e06f14f9", "name": "ggplot2_point", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -3403,7 +3451,7 @@ } }, "tags": [], - "uuid": "0464fb43-deab-405b-bff8-f1f046ddec95" + "uuid": "b1acd066-69e6-4e5c-9b4e-9a7f5a2226e7" }, "tool_id": null, "type": "subworkflow", @@ -3424,7 +3472,7 @@ }, "46": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2", "errors": null, "id": 46, "input_connections": { @@ -3462,15 +3510,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"complement\": \"--complement\", \"cut_type_options\": {\"cut_element\": \"-f\", \"__current_case__\": 0, \"delimiter\": \"\", \"colnames_option\": {\"header\": \"N\", \"__current_case__\": 1, \"list\": [\"3\"]}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.3+galaxy1", + "tool_version": "9.3+galaxy2", "type": "tool", "uuid": "3470d58d-da54-43ef-842c-acfee1b35a56", "when": null, @@ -3515,7 +3563,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md index cac117d0b..29df84c0b 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md @@ -1,5 +1,14 @@ # Changelog +## [0.2.2] 2024-10-14 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1` +- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2` + ## [0.2.1] 2024-08-13 - Expose Busco lineage database parameter From 88379aa210e03421c0dcda99612a16539490bee4 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Wed, 23 Oct 2024 14:17:17 -0400 Subject: [PATCH 2/6] Remove runtime parameters --- .../Assembly-Hifi-only-VGP3.ga | 66 +++---------------- 1 file changed, 9 insertions(+), 57 deletions(-) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga index 31867824e..fbc35a204 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga @@ -329,12 +329,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Cutadapt", - "name": "library" - } - ], + "inputs": [], "label": null, "name": "Cutadapt", "outputs": [ @@ -893,16 +888,7 @@ "output_name": "out1" } }, - "inputs": [ - { - "description": "runtime parameter for tool Hifiasm", - "name": "assembly_options" - }, - { - "description": "runtime parameter for tool Hifiasm", - "name": "mode" - } - ], + "inputs": [], "label": null, "name": "Hifiasm", "outputs": [ @@ -1065,12 +1051,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -1134,12 +1115,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -1203,12 +1179,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -1279,12 +1250,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -1577,16 +1543,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Busco", - "name": "lineage" - }, - { - "description": "runtime parameter for tool Busco", - "name": "lineage_conditional" - } - ], + "inputs": [], "label": null, "name": "Busco", "outputs": [ @@ -1691,12 +1648,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Merqury", - "name": "mode" - } - ], + "inputs": [], "label": null, "name": "Merqury", "outputs": [ @@ -3588,4 +3540,4 @@ ], "uuid": "2988562a-fa7a-4135-bf67-943ab03d1517", "version": 1 -} \ No newline at end of file +} From 8ebe206130bc4927f9c1ba03a010bf17122b2f1f Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Tue, 3 Dec 2024 11:46:09 -0500 Subject: [PATCH 3/6] Change Busco gene predictor to metaeuk --- .../Assembly-Hifi-only-VGP3.ga | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga index fbc35a204..cc26d7aff 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga @@ -1543,7 +1543,7 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ ], "label": null, "name": "Busco", "outputs": [ @@ -1616,7 +1616,7 @@ "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, \"use_augustus\": {\"use_augustus_selector\": \"miniprot\", \"__current_case__\": 1}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"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_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"metaeuk\", \"__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": "5.7.1+galaxy0", "type": "tool", "uuid": "1cd23635-275c-411f-b91d-f53f2bb229cb", @@ -1746,11 +1746,6 @@ "uuid": "da32529d-f84c-4af6-b443-eddfc1705d78", "when": null, "workflow_outputs": [ - { - "label": "Merqury Histograms", - "output_name": "hist_files", - "uuid": "9bb427f1-2afd-4e63-b7a1-2c9b54c6bee0" - }, { "label": "Merqury completeness stats", "output_name": "stats_files", @@ -1760,6 +1755,11 @@ "label": "Merqury png", "output_name": "png_files", "uuid": "1040586b-b0aa-41c3-98e4-00ead4e43a5c" + }, + { + "label": "Merqury Histograms", + "output_name": "hist_files", + "uuid": "9bb427f1-2afd-4e63-b7a1-2c9b54c6bee0" } ] }, @@ -3538,6 +3538,6 @@ "VGP", "Reviewed" ], - "uuid": "2988562a-fa7a-4135-bf67-943ab03d1517", - "version": 1 + "uuid": "e3f8dfb9-0b22-4e7c-a4d6-d333760905f1", + "version": 2 } From 906f445e8b4def41250e87c7c42d9956d573568b Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Tue, 3 Dec 2024 11:53:28 -0500 Subject: [PATCH 4/6] Add busco summary as output --- .../Assembly-Hifi-only-VGP3.ga | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga index cc26d7aff..aa722d2d0 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga @@ -1543,7 +1543,7 @@ "output_name": "output" } }, - "inputs": [ ], + "inputs": [], "label": null, "name": "Busco", "outputs": [ @@ -1573,6 +1573,13 @@ "top": 1426.3228945055312 }, "post_job_actions": { + "RenameDatasetActionbusco_sum": { + "action_arguments": { + "newname": "Busco Summary" + }, + "action_type": "RenameDatasetAction", + "output_name": "busco_sum" + }, "TagDatasetActionbusco_gff": { "action_arguments": { "tags": "#c1,busco_c1_gff" @@ -1622,6 +1629,11 @@ "uuid": "1cd23635-275c-411f-b91d-f53f2bb229cb", "when": null, "workflow_outputs": [ + { + "label": "Busco Summary", + "output_name": "busco_sum", + "uuid": "3d6d5b4e-de88-4a54-ab6f-1a34aae9ecd8" + }, { "label": "Busco summary image", "output_name": "summary_image", @@ -3538,6 +3550,6 @@ "VGP", "Reviewed" ], - "uuid": "e3f8dfb9-0b22-4e7c-a4d6-d333760905f1", - "version": 2 + "uuid": "89098802-f961-4589-894b-79eaf996755b", + "version": 3 } From 50c94d132504ace349b303d7905c094558774bb6 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Tue, 3 Dec 2024 11:55:28 -0500 Subject: [PATCH 5/6] add test for busco --- .../Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml index f00fcbb5b..85856d526 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml @@ -49,6 +49,10 @@ asserts: has_line: line: "# scaffolds 85 1" + Busco Summary: + asserts: + has_text: + line: "C:1.2%[S:1.2%,D:0.0%],F:0.4%,M:98.4%,n:3354" Nx Plot: asserts: has_size: From d90c6f0c9ea17f8924f9459dfbeb02ad8e97f075 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Tue, 3 Dec 2024 11:56:16 -0500 Subject: [PATCH 6/6] correct test --- .../Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml index 85856d526..d2fdf7669 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml @@ -52,7 +52,7 @@ Busco Summary: asserts: has_text: - line: "C:1.2%[S:1.2%,D:0.0%],F:0.4%,M:98.4%,n:3354" + text: "C:1.2%[S:1.2%,D:0.0%],F:0.4%,M:98.4%,n:3354" Nx Plot: asserts: has_size: