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Updating workflows/variant-calling/ploidy-aware-genotype-calling from 0.1.1 to 0.1.2 #1153

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Updating workflows/variant-calling/ploidy-aware-genotype-calling from 0.1.1 to 0.1.2 #1153

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11 changes: 11 additions & 0 deletions workflows/variant-calling/ploidy-aware-genotype-calling/CHANGELOG.md
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@@ -1,5 +1,16 @@
# Changelog

## [0.1.2] - 2026-04-20

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.1.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.3.2+galaxy0`
- `toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.2+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.4+galaxy0`
- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.22+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.22+galaxy2`
- `toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.8` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.9`
- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy3`
- `toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.4+galaxy0`
- `toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/5.4.0c+galaxy0`

## [0.1.1] 2026-03-12

- Rename workflow file to remove '+' character from filename.
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84 changes: 37 additions & 47 deletions workflows/variant-calling/ploidy-aware-genotype-calling/genotype-variant-calling-wgs-pe.ga
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{
"child_steps": [
4,
8,
7,
10,
6,
8,
9
],
"color": "blue",
Expand Down Expand Up @@ -86,7 +86,6 @@
],
"format-version": "0.1",
"license": "MIT",
"release": "0.1.1",
"name": "Paired end variant and ploidy-aware genotype calling",
"readme": "This workflow performs end-to-end germline variant and genotype calling on paired-end Illumina sequencing data from organisms of any given ploidy. Starting from raw FASTQ reads, the workflow handles quality control, read mapping, duplicate removal, variant and genotype calling with FreeBayes, and functional annotation of the resulting variants.",
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Expand Down Expand Up @@ -203,7 +202,7 @@
},
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Expand Down Expand Up @@ -245,16 +244,16 @@
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Expand All @@ -268,7 +267,7 @@
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Expand Down Expand Up @@ -300,16 +299,16 @@
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Expand Down Expand Up @@ -370,7 +369,7 @@
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Expand Down Expand Up @@ -401,24 +400,24 @@
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Expand All @@ -441,16 +440,16 @@
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Expand Down Expand Up @@ -502,7 +501,7 @@
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Expand Down Expand Up @@ -555,16 +554,16 @@
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Expand Down Expand Up @@ -686,7 +685,7 @@
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Expand Down Expand Up @@ -738,16 +737,16 @@
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Expand All @@ -766,7 +765,7 @@
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Expand All @@ -775,12 +774,7 @@
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Expand All @@ -794,16 +788,16 @@
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Expand All @@ -820,12 +814,7 @@
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Expand Down Expand Up @@ -854,7 +843,7 @@
"owner": "nml",
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"type": "tool",
Expand All @@ -874,6 +863,7 @@
"Diploid",
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