diff --git a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md index 98d917a428..435f6b269c 100644 --- a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md @@ -1,5 +1,12 @@ # Changelog +## [0.8.6] - 2026-03-30 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.30+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy2` + ## [0.8.5] - 2026-01-26 ### Manual changes diff --git a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b.ga b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b.ga index 237d4bb273..5f8cf08eb9 100644 --- a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b.ga +++ b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b.ga @@ -15,7 +15,6 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.8.5", "name": "Purging duplicates in one haplotype VGP6b", "report": { "markdown": "Species\n\n```galaxy\nhistory_dataset_embedded(output=\"Species for report\")\n```\n\n\nAssembly\n\n```galaxy\nhistory_dataset_embedded(output=\"Assembly for report\")\n```\n\n\nHaplotype purged\n\n\n```galaxy\nhistory_dataset_embedded(output=\"Haplotype for report\")\n```\n\n\n\n## Merqury results\n\nMerqury QV:\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_QV\")\n```\n\nMerqury completeness:\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_stats\")\n```\n\nMerqury plots:\n\nspectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-cn.fl\")\n```\n\n\nspectra-asm:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-asm.fl\")\n```\n\n\nhap1 spectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_01.spectra-cn.fl\")\n```\n\n\nhap2 spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_02.spectra-cn.fl\")\n```\n\n\n## Compleam results \n\nDatabase:\n\n```galaxy\nhistory_dataset_embedded(output=\"Lineage for report\")\n```\n\n\r\n```galaxy\nhistory_dataset_embedded(output=\"Compleasm on purged Assembly: Summary\")\n```\r\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" @@ -130,14 +129,14 @@ "workflow_outputs": [] }, "4": { - "annotation": "Trimmed PacBio HiFi reads\u2014outputs of cutadapt in the contiging workflow. ", + "annotation": "Trimmed PacBio HiFi reads—outputs of cutadapt in the contiging workflow. ", "content_id": null, "errors": null, "id": 4, "input_connections": {}, "inputs": [ { - "description": "Trimmed PacBio HiFi reads\u2014outputs of cutadapt in the contiging workflow. ", + "description": "Trimmed PacBio HiFi reads—outputs of cutadapt in the contiging workflow. ", "name": "Pacbio Reads Collection - Trimmed" } ], @@ -530,7 +529,7 @@ }, "16": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1+galaxy0", "errors": null, "id": 16, "input_connections": { @@ -559,16 +558,16 @@ "output_name": "out_file1" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "aff5135563c6", + "changeset_revision": "61f9ddbc63ca", "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\": \"1.5*c3\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}, {\"__index__\": 1, \"cond\": \"3*c7\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - 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"tool_version": "1.3.11+galaxy1", + "tool_version": "1.3.11+galaxy2", "type": "tool", "uuid": "a7237fd4-e2ee-4b33-bdb7-975e49ccc16c", "when": null, @@ -1554,7 +1576,12 @@ "output_name": "integer_param" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Purge overlaps", + "name": "function_select" + } + ], "label": null, "name": "Purge overlaps", "outputs": [ @@ -1676,7 +1703,20 @@ "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": [ @@ -1787,7 +1827,16 @@ "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": [ @@ -1886,7 +1935,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Merqury", + "name": "mode" + } + ], "label": null, "name": "Merqury", "outputs": [ @@ -2004,7 +2058,7 @@ }, "35": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy2", "errors": null, "id": 35, "input_connections": { @@ -2040,16 +2094,16 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy2", "tool_shed_repository": { - "changeset_revision": "0fe699ced54f", + "changeset_revision": "10dc0f5a82e2", "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\": false}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "1.3.11+galaxy1", + "tool_version": "1.3.11+galaxy2", "type": "tool", "uuid": "ce91b60e-4bcf-45ff-8334-329f885cc145", "when": null, @@ -2057,7 +2111,7 @@ }, "36": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy2", "errors": null, "id": 36, "input_connections": { @@ -2066,7 +2120,12 @@ "output_name": "get_seqs_purged" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": "Convert purged fasta to gfa", "name": "gfastats", "outputs": [ @@ -2095,16 +2154,16 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy2", "tool_shed_repository": { - "changeset_revision": "0fe699ced54f", + "changeset_revision": "10dc0f5a82e2", "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__\": \"RuntimeValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"yes\", \"__current_case__\": 1, \"terminal_overlaps_length\": \"1000\"}, \"no_sequence\": false, \"discover_paths\": false}, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"RuntimeValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"yes\", \"__current_case__\": 1, \"terminal_overlaps_length\": \"1000\"}, \"no_sequence\": false}, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null, \"discover_paths\": false}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "1.3.11+galaxy1", + "tool_version": "1.3.11+galaxy2", "type": "tool", "uuid": "90cfbc84-a100-4795-a376-f93ffe2dbd0b", "when": null, @@ -2118,7 +2177,7 @@ }, "37": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy2", "errors": null, "id": 37, "input_connections": { @@ -2153,16 +2212,16 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy2", "tool_shed_repository": { - "changeset_revision": "0fe699ced54f", + "changeset_revision": "10dc0f5a82e2", "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\": false}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "1.3.11+galaxy1", + "tool_version": "1.3.11+galaxy2", "type": "tool", "uuid": "ff2b02d1-f6dc-4cd6-bd4a-a70e4d97492c", "when": null, @@ -2301,7 +2360,7 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"busco_database\": {\"__class__\": \"ConnectedValue\"}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}, \"mode\": \"busco\", \"outputs\": [\"full_table_busco\", \"miniprot\", \"translated_protein\", \"full_table\", \"summary\"], \"specified_contigs\": null, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"busco_database\": {\"__class__\": \"ConnectedValue\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}, \"mode\": \"busco\", \"outputs\": [\"full_table_busco\", \"miniprot\", \"translated_protein\", \"full_table\", \"summary\"], \"specified_contigs\": null, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, "tool_version": "0.2.6+galaxy3", "type": "tool", @@ -2810,7 +2869,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.9+galaxy0", "tool_shed_repository": { - "changeset_revision": "d642efa5cbd7", + "changeset_revision": "aaafc0ac4dd2", "name": "datamash_ops", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -2957,7 +3016,7 @@ }, "7": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1+galaxy0", "errors": null, "id": 7, "input_connections": { @@ -2992,16 +3051,16 @@ "output_name": "out_file1" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "aff5135563c6", + "changeset_revision": "61f9ddbc63ca", "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_uuid": null, - "tool_version": "2.1", + "tool_version": "2.1+galaxy0", "type": "tool", "uuid": "8d82104b-65ff-4b66-8df7-09405f70e645", "when": null, @@ -3015,7 +3074,7 @@ } }, "tags": [], - "uuid": "1f630fb0-393d-4c0a-9113-e0a8ba6650f8" + "uuid": "5aad0806-750d-4333-811f-0582f292ad97" }, "tool_id": null, "type": "subworkflow", @@ -3586,7 +3645,7 @@ } }, "tags": [], - "uuid": "b261f8d2-cf22-4ad9-8631-7c2965f64976" + "uuid": "1eb95e35-0cc4-4599-9a2c-cb5a00de8428" }, "tool_id": null, "type": "subworkflow", @@ -3766,6 +3825,7 @@ "tags": [ "VGP_curated" ], - "uuid": "c5c27ce8-b857-4bc2-bdc1-b26eb142bca8", - "version": 3 -} + "uuid": "297aeac2-7431-4df1-a3a0-92c31cab7514", + "version": 1, + "release": "0.8.6" +} \ No newline at end of file