diff --git a/modules/process/sort_bam_samtools.nf b/modules/process/sort_bam_samtools.nf index e917ce8..95a0a2f 100644 --- a/modules/process/sort_bam_samtools.nf +++ b/modules/process/sort_bam_samtools.nf @@ -11,6 +11,6 @@ process SORT_BAM { script: """ - samtools view -@ ${task.cpus} -bh -F 0x200 -F 0x4 | samtools sort -@ ${task.cpus} -o ${bam.baseName}.sorted.bam $bam + samtools view -@ ${task.cpus} -bh -F 0x200 -F 0x4 $bam | samtools sort -@ ${task.cpus} -o ${bam.baseName}.sorted.bam """ -} \ No newline at end of file +}