From 2c427fc14db2c2cbd911bfabf8b94fed24c341b9 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 16 Dec 2024 04:35:57 +0000 Subject: [PATCH] Updating workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3 from 0.2.2 to 0.2.3 --- .../Assembly-Hifi-only-VGP3.ga | 156 ++++++++++++------ .../Assembly-Hifi-only-VGP3/CHANGELOG.md | 7 + 2 files changed, 109 insertions(+), 54 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 aa722d2d0..0df815941 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": "0.2.2", + "release": "0.2.3", "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": [ @@ -871,7 +876,7 @@ }, "23": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.20.0+galaxy0", "errors": null, "id": 23, "input_connections": { @@ -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": [ @@ -958,15 +972,15 @@ "output_name": "raw_unitigs" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.20.0+galaxy0", "tool_shed_repository": { - "changeset_revision": "284a1cb82b61", + "changeset_revision": "5161f204ba63", "name": "hifiasm", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"advanced_options\": {\"advanced_selector\": \"set\", \"__current_case__\": 1, \"hifiasm_kmer_length\": \"51\", \"window_size\": \"51\", \"drop_kmers\": \"5.0\", \"max_overlaps\": \"100\", \"correction_rounds\": \"3\", \"min_hist_cnt\": null, \"max_kocc\": \"20000\", \"hg_size\": \"\"}, \"assembly_options\": {\"assembly_selector\": \"set\", \"__current_case__\": 1, \"cleaning_rounds\": \"4\", \"adapter_length\": \"0\", \"pop_contigs\": \"10000000\", \"pop_unitigs\": \"100000\", \"remove_tips\": \"3\", \"max_overlap\": \"0.8\", \"min_overlap\": \"0.2\", \"disable_post_join\": false, \"ignore_error_corrected\": false, \"hom_cov\": {\"__class__\": \"ConnectedValue\"}}, \"bins_out\": false, \"filter_bits\": {\"__class__\": \"ConnectedValue\"}, \"hic_partition\": {\"hic_partition_selector\": \"blank\", \"__current_case__\": 0}, \"log_out\": true, \"mode\": {\"mode_selector\": \"standard\", \"__current_case__\": 0, \"reads\": {\"__class__\": \"ConnectedValue\"}}, \"ont_integration\": {\"ont_integration_selector\": \"blank\", \"__current_case__\": 0}, \"purge_options\": {\"purge_selector\": \"set\", \"__current_case__\": 1, \"purge_level\": \"0\", \"similarity_threshold\": \"0.75\", \"minimum_overlap\": \"1\", \"purge_max\": null, \"n_hap\": null}, \"scaffolding_options\": {\"scaffold_selector\": \"blank\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.19.9+galaxy0", + "tool_version": "0.20.0+galaxy0", "type": "tool", "uuid": "cecbcd76-97f0-4e7a-9c90-061d3e5be432", "when": null, @@ -1038,7 +1052,7 @@ }, "25": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "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/1.3.8+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "6ec1b853c8fd", + "changeset_revision": "764f2516d837", "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\": \"\", \"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", + "tool_version": "1.3.9+galaxy1", "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/1.3.8+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "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/1.3.8+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "6ec1b853c8fd", + "changeset_revision": "764f2516d837", "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\": \"\", \"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", + "tool_version": "1.3.9+galaxy1", "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/1.3.8+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "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/1.3.8+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "6ec1b853c8fd", + "changeset_revision": "764f2516d837", "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\": \"\", \"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", + "tool_version": "1.3.9+galaxy1", "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/1.3.8+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "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/1.3.8+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "6ec1b853c8fd", + "changeset_revision": "764f2516d837", "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\": \"\", \"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", + "tool_version": "1.3.9+galaxy1", "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/1.3.8+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "errors": null, "id": 29, "input_connections": { @@ -1343,15 +1377,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "6ec1b853c8fd", + "changeset_revision": "764f2516d837", "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": "1.3.8+galaxy0", + "tool_version": "1.3.9+galaxy1", "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/1.3.8+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "errors": null, "id": 30, "input_connections": { @@ -1400,15 +1434,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "6ec1b853c8fd", + "changeset_revision": "764f2516d837", "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": "1.3.8+galaxy0", + "tool_version": "1.3.9+galaxy1", "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/1.3.8+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "errors": null, "id": 31, "input_connections": { @@ -1458,15 +1492,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "6ec1b853c8fd", + "changeset_revision": "764f2516d837", "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": "1.3.8+galaxy0", + "tool_version": "1.3.9+galaxy1", "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/1.3.8+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "errors": null, "id": 32, "input_connections": { @@ -1510,15 +1544,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "6ec1b853c8fd", + "changeset_revision": "764f2516d837", "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": "1.3.8+galaxy0", + "tool_version": "1.3.9+galaxy1", "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/5.7.1+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+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": [ @@ -1616,15 +1659,15 @@ "output_name": "summary_image" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0", "tool_shed_repository": { - "changeset_revision": "2babe6d5c561", + "changeset_revision": "e5c372c91e46", "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, \"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", + "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__\": \"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": "5.8.0+galaxy0", "type": "tool", "uuid": "1cd23635-275c-411f-b91d-f53f2bb229cb", "when": null, @@ -1660,7 +1703,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Merqury", + "name": "mode" + } + ], "label": null, "name": "Merqury", "outputs": [ @@ -2239,7 +2287,7 @@ } }, "tags": [], - "uuid": "8e50f47e-494e-44ae-af08-e31da30a873e" + "uuid": "e19c7532-c964-4393-a74c-2204a76d2bd5" }, "tool_id": null, "type": "subworkflow", @@ -2621,7 +2669,7 @@ } }, "tags": [], - "uuid": "f888dd45-2f79-45f9-83d6-dbe483be29a3" + "uuid": "8fc5f09e-7cd9-4800-a6d2-a7deefc3955b" }, "tool_id": null, "type": "subworkflow", @@ -3415,7 +3463,7 @@ } }, "tags": [], - "uuid": "b1acd066-69e6-4e5c-9b4e-9a7f5a2226e7" + "uuid": "18a9ca3b-0d5c-4cc7-abaa-83c0214f503a" }, "tool_id": null, "type": "subworkflow", @@ -3552,4 +3600,4 @@ ], "uuid": "89098802-f961-4589-894b-79eaf996755b", "version": 3 -} +} \ No newline at end of file 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 29df84c0b..cb0bbaa65 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 +1,12 @@ # Changelog +## [0.2.3] 2024-12-16 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.20.0+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0` + ## [0.2.2] 2024-10-14 ### Automatic update