diff --git a/workflows/microbiome/metagenomic-genes-catalogue/CHANGELOG.md b/workflows/microbiome/metagenomic-genes-catalogue/CHANGELOG.md index 65abca3e8f..eb9a915844 100644 --- a/workflows/microbiome/metagenomic-genes-catalogue/CHANGELOG.md +++ b/workflows/microbiome/metagenomic-genes-catalogue/CHANGELOG.md @@ -1,5 +1,13 @@ # Changelog +## [1.4] - 2026-08-10 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/amrfinderplus/amrfinderplus/3.12.8+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/amrfinderplus/amrfinderplus/4.2.7+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.4.0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.4.0+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/coverm_contig/coverm_contig/0.8.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/coverm_contig/coverm_contig/0.8.0+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy2` + ## [1.3] - 2026-07-16 ### Changed diff --git a/workflows/microbiome/metagenomic-genes-catalogue/metagenomic-genes-catalogue.ga b/workflows/microbiome/metagenomic-genes-catalogue/metagenomic-genes-catalogue.ga index f56cf22277..9d0be46f44 100644 --- a/workflows/microbiome/metagenomic-genes-catalogue/metagenomic-genes-catalogue.ga +++ b/workflows/microbiome/metagenomic-genes-catalogue/metagenomic-genes-catalogue.ga @@ -53,13 +53,13 @@ }, { "child_steps": [ - 27, 18, 19, 20, 21, 22, - 24 + 24, + 27 ], "color": "red", "data": { @@ -78,13 +78,13 @@ }, { "child_steps": [ - 12, 7, 10, 13, 14, 15, - 9 + 9, + 12 ], "color": "turquoise", "data": { @@ -650,12 +650,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Add input name as column", - "name": "input" - } - ], + "inputs": [], "label": null, "name": "Add input name as column", "outputs": [ @@ -676,7 +671,7 @@ "owner": "mvdbeek", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"header\": {\"contains_header\": \"no\", \"__current_case__\": 1}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"prepend\": true, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"header\": {\"contains_header\": \"no\", \"__current_case__\": 1}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"prepend\": true, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, "tool_version": "0.3.0", "type": "tool", @@ -1002,7 +997,7 @@ }, "18": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/amrfinderplus/amrfinderplus/3.12.8+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/amrfinderplus/amrfinderplus/4.2.7+galaxy0", "errors": null, "id": 18, "input_connections": { @@ -1053,16 +1048,16 @@ "output_name": "nucleotide_output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/amrfinderplus/amrfinderplus/3.12.8+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/amrfinderplus/amrfinderplus/4.2.7+galaxy0", "tool_shed_repository": { - "changeset_revision": "573cfe217474", + "changeset_revision": "96112e4c5e26", "name": "amrfinderplus", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_option\": {\"amrfinder_db_select\": {\"__class__\": \"ConnectedValue\"}, \"input_mode\": {\"input_select\": \"nucleotide\", \"__current_case__\": 0, \"nucleotide_input\": {\"__class__\": \"ConnectedValue\"}, \"nucleotide_flank5_size\": \"0\"}}, \"options\": {\"ident_min\": \"-1.0\", \"coverage_min\": \"0.5\", \"translation_table\": \"11\", \"plus\": false, \"report_all_equal\": false, \"print_node\": false, \"name\": null}, \"organism_options\": {\"organism_conditionnal\": {\"organism_select\": \"\", \"__current_case__\": 1}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"input_option\": {\"amrfinder_db_select\": {\"__class__\": \"ConnectedValue\"}, \"input_mode\": {\"input_select\": \"nucleotide\", \"__current_case__\": 0, \"nucleotide_input\": {\"__class__\": \"ConnectedValue\"}, \"nucleotide_flank5_size\": \"0\"}}, \"options\": {\"ident_min\": \"-1.0\", \"coverage_min\": \"0.5\", \"translation_table\": \"11\", \"plus\": false, \"report_all_equal\": false, \"print_node\": false, \"name\": null, \"add_version_columns\": false}, \"organism_options\": {\"organism_conditionnal\": {\"organism_select\": \"\", \"__current_case__\": 1}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "3.12.8+galaxy0", + "tool_version": "4.2.7+galaxy0", "type": "tool", "uuid": "b0f0dda9-e4aa-449f-8e90-d9b577e7310e", "when": null, @@ -1076,7 +1071,7 @@ }, "19": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.4.0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.4.0+galaxy1", "errors": null, "id": 19, "input_connections": { @@ -1116,16 +1111,16 @@ "output_name": "report" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.4.0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.4.0+galaxy1", "tool_shed_repository": { - "changeset_revision": "31f58ec0459a", + "changeset_revision": "d8b0de0554a9", "name": "abricate", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"adv\": {\"db\": {\"__class__\": \"ConnectedValue\"}, \"no_header\": false, \"min_dna_id\": \"80.0\", \"min_cov\": \"80.0\"}, \"file_input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "1.4.0", + "tool_version": "1.4.0+galaxy1", "type": "tool", "uuid": "f0068a6e-6249-45bd-8afd-4f42615b3f97", "when": null, @@ -1431,7 +1426,7 @@ "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0", "tool_shed_repository": { - "changeset_revision": "2040e4c2750a", + "changeset_revision": "6428adb323eb", "name": "column_remove_by_header", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1532,7 +1527,7 @@ "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0", "tool_shed_repository": { - "changeset_revision": "2040e4c2750a", + "changeset_revision": "6428adb323eb", "name": "column_remove_by_header", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -2465,14 +2460,14 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy3", "tool_shed_repository": { - "changeset_revision": "c41d78ae5fee", + "changeset_revision": "ab83aa685821", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"column1\": \"1\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": false, \"ignore_case\": false, \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \" \", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "9.5+galaxy2", + "tool_version": "9.5+galaxy3", "type": "tool", "uuid": "75d1671c-22d9-438f-8eae-f86e01cc2f8a", "when": null, @@ -2569,12 +2564,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Tabular-to-FASTA", - "name": "input" - } - ], + "inputs": [], "label": null, "name": "Tabular-to-FASTA", "outputs": [ @@ -2610,7 +2600,7 @@ "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"seq_col\": \"4\", \"title_col\": [\"1\"], \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"seq_col\": \"4\", \"title_col\": [\"1\"], \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, "tool_version": "1.1.1", "type": "tool", @@ -2666,14 +2656,14 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy3", "tool_shed_repository": { - "changeset_revision": "c41d78ae5fee", + "changeset_revision": "ab83aa685821", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"infile\": {\"__class__\": \"ConnectedValue\"}, \"replacements\": [{\"__index__\": 0, \"find_pattern\": \"^>([^ ]+)_# \", \"replace_pattern\": \">\\\\1 # \", \"sed_options\": null}], \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "9.5+galaxy2", + "tool_version": "9.5+galaxy3", "type": "tool", "uuid": "0db8d26f-1e31-482f-af38-c454217c3a2d", "when": null, @@ -2826,7 +2816,7 @@ } }, "tags": [], - "uuid": "80a15f5a-6c9c-477b-b3a5-b139a5e6c15e" + "uuid": "69a7b522-f940-4cf3-9b3f-4c850edb3498" }, "tool_id": null, "type": "subworkflow", @@ -2872,7 +2862,7 @@ "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0", "tool_shed_repository": { - "changeset_revision": "2040e4c2750a", + "changeset_revision": "6428adb323eb", "name": "column_remove_by_header", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -3404,7 +3394,7 @@ }, "38": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/coverm_contig/coverm_contig/0.8.0+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/coverm_contig/coverm_contig/0.8.0+galaxy1", "errors": null, "id": 38, "input_connections": { @@ -3439,16 +3429,16 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/coverm_contig/coverm_contig/0.8.0+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/coverm_contig/coverm_contig/0.8.0+galaxy1", "tool_shed_repository": { - "changeset_revision": "d9b724b4a136", + "changeset_revision": "66919d81c4d1", "name": "coverm_contig", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"alignment\": {\"min_read_aligned_length\": \"0\", \"min_read_percent_identity\": \"0.0\", \"min_read_aligned_percent\": \"0.0\", \"proper_pairs_only\": {\"proper_pairs_only\": \"\", \"__current_case__\": 1}, \"exclude_supplementary\": false}, \"cov\": {\"methods\": \"mean\", \"trim_min\": \"5\", \"trim_max\": \"95\", \"min_covered_fraction\": \"10\", \"contig_end_exclusion\": \"75\"}, \"mapped\": {\"mapped\": \"not-mapped\", \"__current_case__\": 1, \"mode\": {\"mode\": \"individual\", \"__current_case__\": 0, \"read_type\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"paired_reads\": {\"__class__\": \"ConnectedValue\"}}, \"reference\": {\"__class__\": \"ConnectedValue\"}}, \"mapper\": \"minimap2-sr\"}, \"output_format\": \"dense\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "0.8.0+galaxy0", + "tool_version": "0.8.0+galaxy1", "type": "tool", "uuid": "d42bbc13-69c8-4eb6-b060-cb81ebb44924", "when": null, @@ -3594,7 +3584,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "e9005d1f3cfd", + "changeset_revision": "7d01da0b9e18", "name": "taxonomy_krona_chart", "owner": "crs4", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -3615,7 +3605,7 @@ }, "42": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy2", "errors": null, "id": 42, "input_connections": { @@ -3679,16 +3669,16 @@ "output_name": "html_report" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy2", "tool_shed_repository": { - "changeset_revision": "fac2260bc88a", + "changeset_revision": "0559e0711094", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"image_content_input\": {\"__class__\": \"RuntimeValue\"}, \"png_plots\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"quast\", \"__current_case__\": 22, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 54, \"plot_type\": \"table\", \"section_name\": \"ABRicate report\", \"title\": null, \"description\": null, \"xlab\": null, \"ylab\": null, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 54, \"plot_type\": \"table\", \"section_name\": \"AMRFinderPlus report with argNorm\", \"title\": null, \"description\": null, \"xlab\": null, \"ylab\": null, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 3, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 54, \"plot_type\": \"table\", \"section_name\": \"starAMR detailed report\", \"title\": null, \"description\": null, \"xlab\": null, \"ylab\": null, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 4, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 54, \"plot_type\": \"table\", \"section_name\": \"CoverM\", \"title\": null, \"description\": null, \"xlab\": null, \"ylab\": null, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 5, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 54, \"plot_type\": \"table\", \"section_name\": \"EggnogMapper annotations\", \"title\": null, \"description\": null, \"xlab\": null, \"ylab\": null, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 6, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 54, \"plot_type\": \"table\", \"section_name\": \"MMseqs2 taxonomy\", \"title\": null, \"description\": null, \"xlab\": null, \"ylab\": null, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"title\": \"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"image_content_input\": {\"__class__\": \"RuntimeValue\"}, \"png_plots\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"quast\", \"__current_case__\": 22, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 55, \"plot_type\": \"table\", \"section_name\": \"ABRicate report\", \"title\": null, \"description\": null, \"xlab\": null, \"ylab\": null, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 55, \"plot_type\": \"table\", \"section_name\": \"AMRFinderPlus report with argNorm\", \"title\": null, \"description\": null, \"xlab\": null, \"ylab\": null, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 3, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 55, \"plot_type\": \"table\", \"section_name\": \"starAMR detailed report\", \"title\": null, \"description\": null, \"xlab\": null, \"ylab\": null, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 4, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 55, \"plot_type\": \"table\", \"section_name\": \"CoverM\", \"title\": null, \"description\": null, \"xlab\": null, \"ylab\": null, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 5, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 55, \"plot_type\": \"table\", \"section_name\": \"EggnogMapper annotations\", \"title\": null, \"description\": null, \"xlab\": null, \"ylab\": null, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 6, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 55, \"plot_type\": \"table\", \"section_name\": \"MMseqs2 taxonomy\", \"title\": null, \"description\": null, \"xlab\": null, \"ylab\": null, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"title\": \"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "1.35+galaxy1", + "tool_version": "1.35+galaxy2", "type": "tool", "uuid": "003f4529-b21a-47fa-b0dd-dec70c091e28", "when": null, @@ -3708,7 +3698,7 @@ "genes-collection", "paired-collection(s)" ], - "uuid": "8c7039c9-333f-47dc-ae7d-2985935a8c8d", + "uuid": "dc82e32d-39db-4517-883e-e9e05a38186f", "version": 1, - "release": "1.3" + "release": "1.4" } \ No newline at end of file