diff --git a/modules/samtools/merge/main.nf b/modules/samtools/merge/main.nf index 81b2828c..23b31e2f 100644 --- a/modules/samtools/merge/main.nf +++ b/modules/samtools/merge/main.nf @@ -22,14 +22,14 @@ process SAMTOOLS_MERGE { tuple val(meta), path(bams) output: - tuple val(meta), path("*merged.bam"), emit: merged_bam - path "*.version.txt" , emit: version + tuple val(meta), path("${prefix}.bam"), emit: bam + path "*.version.txt" , emit: version script: def software = getSoftwareName(task.process) - def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ - samtools merge ${prefix}_merged.bam $bams + samtools merge ${prefix}.bam $bams echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt """ } diff --git a/tests/modules/samtools/merge/main.nf b/tests/modules/samtools/merge/main.nf index 75ba886b..a4511a34 100644 --- a/tests/modules/samtools/merge/main.nf +++ b/tests/modules/samtools/merge/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_MERGE } from '../../../../modules/samtools/merge/main.nf' addParams( options: [:] ) +include { SAMTOOLS_MERGE } from '../../../../modules/samtools/merge/main.nf' addParams( options: [suffix:'_merged'] ) workflow test_samtools_merge { input = [ [ id: 'test' ], // meta map