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added default -doMajorMinor 1 to output angsd beagle format #690

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Mar 10, 2021
Merged

added default -doMajorMinor 1 to output angsd beagle format #690

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added default -doMajorMinor 1 to output angsd beagle format + correct…
alexandregilardet Mar 8, 2021
069267a
Changed CHANGELOG.md for #690
alexandregilardet Mar 9, 2021
178b23a
Merge branch 'dev' into master
alexandregilardet Mar 9, 2021
2185f79
corrected CHANGELOG.md dev section
alexandregilardet Mar 10, 2021
cb84882
corrected CHANGELOG.md dev section
alexandregilardet Mar 10, 2021
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -21,9 +21,12 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- Added exit code `140` to re-tryable exit code list to account for certain scheduler wall-time limit fails.
- [672](https://github.com/nf-core/eager/issues/672) - Removed java parameter from picard tools which could cause memory issues
- [679](https://github.com/nf-core/eager/issues/679) - Refactor within-process bash conditions to groovy/nextflow, due to incompatibility with some servers environments
- [#690](https://github.com/nf-core/eager/pull/690) - Fixed ANGSD output mode for beagle by setting `-doMajorMinor 1` as default in that case

### `Dependencies`

- Bumped MultiQC to 1.10 for improved functionality

### `Deprecated`

## [2.3.1] - 2021-01-14
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5 changes: 3 additions & 2 deletions main.nf
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Expand Up @@ -463,7 +463,7 @@ if (params.run_genotyping){
}

if (params.genotyping_tool == 'angsd' && ! ( params.angsd_glformat == 'text' || params.angsd_glformat == 'binary' || params.angsd_glformat == 'binary_three' || params.angsd_glformat == 'beagle' ) ) {
exit 1, "[nf-core/eager] error: please check your ANGSD genotyping model! Options: 'text', 'binary', 'binary_three', 'beagle'. Found parameter: --angsd_glmodel '${params.angsd_glmodel}'."
exit 1, "[nf-core/eager] error: please check your ANGSD output format! Options: 'text', 'binary', 'binary_three', 'beagle'. Found parameter: --angsd_glformat '${params.angsd_glformat}'."
}

if ( !params.angsd_createfasta && params.angsd_fastamethod != 'random' ) {
Expand Down Expand Up @@ -2836,10 +2836,11 @@ process genotyping_angsd {
}

def angsd_fasta = !params.angsd_createfasta ? '' : params.angsd_fastamethod == 'random' ? '-doFasta 1 -doCounts 1' : '-doFasta 2 -doCounts 1'
def angsd_majorminor = params.angsd_glformat != "beagle" ? '' : '-doMajorMinor 1'
"""
echo ${bam} > bam.filelist
mkdir angsd
angsd -bam bam.filelist -nThreads ${task.cpus} -GL ${angsd_glmodel} -doGlF ${angsd_glformat} ${angsd_fasta} -out ${samplename}.angsd
angsd -bam bam.filelist -nThreads ${task.cpus} -GL ${angsd_glmodel} -doGlF ${angsd_glformat} ${angsd_majorminor} ${angsd_fasta} -out ${samplename}.angsd
"""
}

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