diff --git a/workflows/bacterial_genomics/bacterial-quality-and-contamination-control-post-assembly/CHANGELOG.md b/workflows/bacterial_genomics/bacterial-quality-and-contamination-control-post-assembly/CHANGELOG.md index 45e0ce9ab6..e14bf4e361 100644 --- a/workflows/bacterial_genomics/bacterial-quality-and-contamination-control-post-assembly/CHANGELOG.md +++ b/workflows/bacterial_genomics/bacterial-quality-and-contamination-control-post-assembly/CHANGELOG.md @@ -1,5 +1,13 @@ # Changelog +## [1.0.2] - 2025-10-07 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/checkm2/checkm2/1.0.2+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/checkm2/checkm2/1.1.0+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.0+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.1+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.0+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.1+galaxy0` + ## [1.0.1] - 2025-08-25 ### Automatic update diff --git a/workflows/bacterial_genomics/bacterial-quality-and-contamination-control-post-assembly/bacterial_quality_and_contamination_control_post_assembly.ga b/workflows/bacterial_genomics/bacterial-quality-and-contamination-control-post-assembly/bacterial_quality_and_contamination_control_post_assembly.ga index d0b0be3617..771daba098 100644 --- a/workflows/bacterial_genomics/bacterial-quality-and-contamination-control-post-assembly/bacterial_quality_and_contamination_control_post_assembly.ga +++ b/workflows/bacterial_genomics/bacterial-quality-and-contamination-control-post-assembly/bacterial_quality_and_contamination_control_post_assembly.ga @@ -337,7 +337,7 @@ }, "9": { "annotation": "quast_quality_fasta", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy1", "errors": null, "id": 9, "input_connections": { @@ -405,15 +405,15 @@ "output_name": "report_tabular" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy1", "tool_shed_repository": { - "changeset_revision": "a3b35edea53a", + "changeset_revision": "1b1cf0c96501", "name": "quast", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"advanced\": {\"contig_thresholds\": \"0,200,500,1000\", \"strict_NA\": false, \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": true, \"fragmented_max_indent\": null, \"report_all_metrics\": false, \"x_for_Nx\": \"90\"}, \"alignments\": {\"use_all_alignments\": false, \"min_alignment\": \"65\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": false, \"upper_bound_assembly\": false, \"upper_bound_min_con\": null, \"local_mis_size\": \"200\"}, \"assembly\": {\"type\": \"genome\", \"__current_case__\": 0, \"ref\": {\"use_ref\": \"false\", \"__current_case__\": 1, \"est_ref_size\": null}, \"orga_type\": \"\", \"min_identity\": \"95.0\"}, \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": false, \"conserved_genes_finding\": true}, \"large\": false, \"min_contig\": \"200\", \"mode\": {\"mode\": \"individual\", \"__current_case__\": 0, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"reads\": {\"reads_option\": \"disabled\", \"__current_case__\": 0}}, \"output_files\": [\"html\", \"pdf\", \"tabular\", \"log\", \"summary\", \"krona\"], \"split_scaffolds\": false, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", - "tool_version": "5.3.0+galaxy0", + "tool_version": "5.3.0+galaxy1", "type": "tool", "uuid": "36d6441b-1a1d-458d-be2d-698255c33a2f", "when": "$(inputs.when)", @@ -432,7 +432,7 @@ }, "10": { "annotation": "Checkm2 to predict the completeness and contamination in an assembly", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/checkm2/checkm2/1.0.2+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/checkm2/checkm2/1.1.0+galaxy0", "errors": null, "id": 10, "input_connections": { @@ -485,15 +485,15 @@ "output_name": "quality" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/checkm2/checkm2/1.0.2+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/checkm2/checkm2/1.1.0+galaxy0", "tool_shed_repository": { - "changeset_revision": "66acaec9f386", + "changeset_revision": "304ac5b49dea", "name": "checkm2", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"database\": \"1.0.2\", \"genes\": false, \"input\": {\"__class__\": \"ConnectedValue\"}, \"model\": \"--allmodels\", \"ttable\": \"11\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.0.2+galaxy1", + "tool_version": "1.1.0+galaxy0", "type": "tool", "uuid": "ba0ba299-26bc-42b1-a49b-50efb25cc08b", "when": null, @@ -595,7 +595,7 @@ }, "12": { "annotation": "quast_quality_fastq", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy1", "errors": null, "id": 12, "input_connections": { @@ -671,15 +671,15 @@ "output_name": "report_tabular" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy1", "tool_shed_repository": { - "changeset_revision": "a3b35edea53a", + "changeset_revision": "1b1cf0c96501", "name": "quast", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"advanced\": {\"contig_thresholds\": \"0,200,500,1000\", \"strict_NA\": false, \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": true, \"fragmented_max_indent\": null, \"report_all_metrics\": false, \"x_for_Nx\": \"90\"}, \"alignments\": {\"use_all_alignments\": false, \"min_alignment\": \"65\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": false, \"upper_bound_assembly\": false, \"upper_bound_min_con\": null, \"local_mis_size\": \"200\"}, \"assembly\": {\"type\": \"genome\", \"__current_case__\": 0, \"ref\": {\"use_ref\": \"false\", \"__current_case__\": 1, \"est_ref_size\": null}, \"orga_type\": \"\", \"min_identity\": \"95.0\"}, \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": false, \"conserved_genes_finding\": true}, \"large\": false, \"min_contig\": \"200\", \"mode\": {\"mode\": \"individual\", \"__current_case__\": 0, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"reads\": {\"reads_option\": \"paired\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"input_2\": {\"__class__\": \"ConnectedValue\"}}}, \"output_files\": [\"html\", \"pdf\", \"tabular\", \"log\", \"summary\", \"krona\"], \"split_scaffolds\": false, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", - "tool_version": "5.3.0+galaxy0", + "tool_version": "5.3.0+galaxy1", "type": "tool", "uuid": "5b312a7e-4f4a-479d-a2ac-fbb379ef67ee", "when": "$(inputs.when)", @@ -1082,7 +1082,7 @@ }, "19": { "annotation": "ToolDistillator extracts results from tools and creates a JSON file for each tool", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.0+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.1+galaxy0", "errors": null, "id": 19, "input_connections": { @@ -1169,15 +1169,15 @@ "output_name": "output_json" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.0+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "c6b5c2975e51", + "changeset_revision": "bbdc53e9b559", "name": "tooldistillator", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"log\": false, \"tool_section\": {\"tools\": [{\"__index__\": 0, \"select_tool\": {\"tool_list\": \"kraken2\", \"__current_case__\": 23, \"input\": {\"__class__\": \"ConnectedValue\"}, \"seq_classification_file_path\": {\"__class__\": \"ConnectedValue\"}, \"origin\": {\"origin\": \"false\", \"__current_case__\": 1}, \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"select_tool\": {\"tool_list\": \"bracken\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}, \"origin\": {\"origin\": \"false\", \"__current_case__\": 1}, \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}, \"kraken_report_path\": {\"__class__\": \"ConnectedValue\"}, \"threshold\": null, \"read_len\": \"100\", \"level\": \"S\"}}, {\"__index__\": 2, \"select_tool\": {\"tool_list\": \"recentrifuge\", \"__current_case__\": 34, \"input\": {\"__class__\": \"ConnectedValue\"}, \"rcf_stat_path\": {\"__class__\": \"ConnectedValue\"}, \"rcf_html_path\": {\"__class__\": \"ConnectedValue\"}, \"origin\": {\"origin\": \"false\", \"__current_case__\": 1}, \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 3, \"select_tool\": {\"tool_list\": \"quast\", \"__current_case__\": 33, \"input\": {\"__class__\": \"ConnectedValue\"}, \"quast_html_path\": {\"__class__\": \"ConnectedValue\"}, \"origin\": {\"origin\": \"true\", \"__current_case__\": 0, \"analysis_software_version\": null}, \"reference_database_version\": null}}, {\"__index__\": 4, \"select_tool\": {\"tool_list\": \"checkm2\", \"__current_case__\": 7, \"input\": {\"__class__\": \"ConnectedValue\"}, \"diamond_results_path\": {\"__class__\": \"ConnectedValue\"}, \"protein_zip_path\": {\"__class__\": \"ConnectedValue\"}, \"checkm2_log_path\": {\"__class__\": \"RuntimeValue\"}, \"origin\": {\"origin\": \"true\", \"__current_case__\": 0, \"analysis_software_version\": null}, \"reference_database_version\": null}}]}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.0.0+galaxy1", + "tool_version": "1.0.1+galaxy0", "type": "tool", "uuid": "b9df0d7d-1411-439a-91f2-6eafcb8d1bff", "when": null, @@ -1191,7 +1191,7 @@ }, "20": { "annotation": "ToolDistillator summarize groups all JSON file into a unique JSON file", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.0+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.1+galaxy0", "errors": null, "id": 20, "input_connections": { @@ -1222,15 +1222,15 @@ "output_name": "summary_json" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.0+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "3d0223265277", + "changeset_revision": "bbbcee71e70e", "name": "tooldistillator_summarize", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"summarize_data\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.0.0+galaxy1", + "tool_version": "1.0.1+galaxy0", "type": "tool", "uuid": "2da488a2-bb25-49d6-9877-76c58d9d97e9", "when": null, @@ -1251,7 +1251,7 @@ "ABRomics", "fasta" ], - "uuid": "8911f5cd-67b1-4d57-be62-abe84ca07f23", + "uuid": "0bebecd6-090c-4b08-91d7-758a927a9a2d", "version": 1, - "release": "1.0.1" + "release": "1.0.2" } \ No newline at end of file