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Corrected sort

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This commit is contained in:
sruthipsuresh 2021-01-08 13:54:56 -06:00
parent 70de0331a5
commit 29639c522f
2 changed files with 3 additions and 2 deletions
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4
software/bedtools/sort/main.nf
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@ -21,14 +21,14 @@ process BEDTOOLS_SORT {
tuple val(meta), path(beds)
output:
tuple val(meta), path("*.sort"), emit: sort
tuple val(meta), path("*.sort.bed"), emit: sort
path "*.version.txt", emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
bedtools sort -i $beds ${options.args} > ${prefix}.sort
bedtools sort -i $beds ${options.args} > ${prefix}.sort.bed
bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt
"""
}

1
tests/software/bedtools/main.nf
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@ -77,6 +77,7 @@ workflow test_bedtools_sort {
file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true) ]
BEDTOOLS_SORT( input )
}