diff --git a/software/bedtools/sort/main.nf b/software/bedtools/sort/main.nf index 3c490131..9ff7fda9 100644 --- a/software/bedtools/sort/main.nf +++ b/software/bedtools/sort/main.nf @@ -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" > ${software}.version.txt """ } diff --git a/tests/software/bedtools/main.nf b/tests/software/bedtools/main.nf index dd71b960..611f2b8c 100644 --- a/tests/software/bedtools/main.nf +++ b/tests/software/bedtools/main.nf @@ -77,6 +77,7 @@ workflow test_bedtools_sort { file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true) ] BEDTOOLS_SORT( input ) + }