diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling/CHANGELOG.md b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling/CHANGELOG.md index 79dd9e0ae..721dd3533 100644 --- a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling/CHANGELOG.md +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling/CHANGELOG.md @@ -1,5 +1,17 @@ # Changelog +## [0.2.5] 2024-11-18 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18` +- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.3` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5` +- `toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0` +- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3` + ## [0.2.4] 2023-11-20 - Fix author in dockstore diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling/pe-wgs-variation.ga b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling/pe-wgs-variation.ga index 9a814598b..e4dbd1b2d 100644 --- a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling/pe-wgs-variation.ga +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling/pe-wgs-variation.ga @@ -11,7 +11,7 @@ "format-version": "0.1", "license": "MIT", "name": "COVID-19: variation analysis on WGS PE data", - "release": "0.2.4", + "release": "0.2.5", "steps": { "0": { "annotation": "Illumina reads with fastqsanger encoding", @@ -29,20 +29,15 @@ "name": "Input dataset collection", "outputs": [], "position": { - "bottom": 531.03125, - "height": 81, - "left": -513, - "right": -313, - "top": 450.03125, - "width": 200, - "x": -513, - "y": 450.03125 + "left": 0, + "top": 300.5625 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"fastqsanger\", \"fastqsanger.gz\"], \"collection_type\": \"list:paired\"}", + "tool_state": "{\"optional\": false, \"format\": [\"fastqsanger\", \"fastqsanger.gz\"], \"tag\": null, \"collection_type\": \"list:paired\"}", "tool_version": null, "type": "data_collection_input", "uuid": "b21522ed-fd9a-44b6-8ed3-a8640727961d", + "when": null, "workflow_outputs": [] }, "1": { @@ -61,25 +56,20 @@ "name": "Input dataset", "outputs": [], "position": { - 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