diff --git a/modules/picard/sortsam/main.nf b/modules/picard/sortsam/main.nf index dc2a8136..2af28496 100644 --- a/modules/picard/sortsam/main.nf +++ b/modules/picard/sortsam/main.nf @@ -24,7 +24,7 @@ process PICARD_SORTSAM { val sort_order output: - tuple val(meta), path("*.sorted.bam"), emit: bam + tuple val(meta), path("*.bam"), emit: bam path "*.version.txt" , emit: version script: @@ -41,7 +41,7 @@ process PICARD_SORTSAM { SortSam \\ -Xmx${avail_mem}g \\ --INPUT $bam \\ - --OUTPUT ${prefix}.sorted.bam \\ + --OUTPUT ${prefix}.bam \\ --SORT_ORDER $sort_order echo \$(picard SortSam --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d: > ${software}.version.txt diff --git a/tests/modules/picard/sortsam/main.nf b/tests/modules/picard/sortsam/main.nf index 71ae75d6..0130fad6 100644 --- a/tests/modules/picard/sortsam/main.nf +++ b/tests/modules/picard/sortsam/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_SORTSAM } from '../../../../modules/picard/sortsam/main.nf' addParams( options: [:] ) +include { PICARD_SORTSAM } from '../../../../modules/picard/sortsam/main.nf' addParams( options: [suffix:'.sorted'] ) workflow test_picard_sortsam {