From 402f0fe9839e121f2a7c18f0ad82f65b5880b51a Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 10 Feb 2025 05:59:22 +0000 Subject: [PATCH] Updating workflows/virology/influenza-isolates-consensus-and-subtyping from 0.1 to 0.2 --- .../CHANGELOG.md | 10 ++++ .../influenza-consensus-and-subtyping.ga | 60 +++++++++---------- 2 files changed, 40 insertions(+), 30 deletions(-) diff --git a/workflows/virology/influenza-isolates-consensus-and-subtyping/CHANGELOG.md b/workflows/virology/influenza-isolates-consensus-and-subtyping/CHANGELOG.md index 5eae98720..e4ad59ed5 100644 --- a/workflows/virology/influenza-isolates-consensus-and-subtyping/CHANGELOG.md +++ b/workflows/virology/influenza-isolates-consensus-and-subtyping/CHANGELOG.md @@ -1,5 +1,15 @@ # Changelog +## [0.2] 2025-02-10 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy4` +- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.520+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.526+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/2.3.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/2.3.6+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/snipit/snipit/1.2+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/snipit/snipit/1.6+galaxy0` + ## [0.1] 2025-01-09 First release. diff --git a/workflows/virology/influenza-isolates-consensus-and-subtyping/influenza-consensus-and-subtyping.ga b/workflows/virology/influenza-isolates-consensus-and-subtyping/influenza-consensus-and-subtyping.ga index 64d877062..a74d8b059 100644 --- a/workflows/virology/influenza-isolates-consensus-and-subtyping/influenza-consensus-and-subtyping.ga +++ b/workflows/virology/influenza-isolates-consensus-and-subtyping/influenza-consensus-and-subtyping.ga @@ -163,7 +163,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.1", + "release": "0.2", "name": "Influenza A isolate subtyping and consensus sequence generation", "report": { "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" @@ -270,7 +270,7 @@ }, "3": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy4", "errors": null, "id": 3, "input_connections": { @@ -322,15 +322,15 @@ "output_name": "report_html" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy4", "tool_shed_repository": { - "changeset_revision": "c59d48774d03", + "changeset_revision": "10678d49d39e", "name": "fastp", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": \"30\", \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": false}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": \"\", \"umi_len\": null, \"umi_prefix\": \"\"}, \"cutting_by_quality_options\": {\"cut_by_quality5\": true, \"cut_by_quality3\": true, \"cut_window_size\": null, \"cut_mean_quality\": \"30\"}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"paired_collection\", \"__current_case__\": 2, \"paired_input\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": \"\", \"adapter_sequence2\": \"\"}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - 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