Write samtools collate output to file to avoid filling up /tmp (#47)

BCCDC-PHL · Jan 24, 2022 · f1e4160 · f1e4160
1 parent 9d6c711
commit f1e4160
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/modules/utils.nf b/modules/utils.nf
@@ -55,8 +55,8 @@ process downsampledBamToFastq {
 
     script:
         """
-        samtools collate -u -O ${downsampled_bam} | \
-        samtools fastq -n -0 /dev/null -1 ${sampleId}_hostfiltered_downsampled_R1.fastq.gz -2 ${sampleId}_hostfiltered_downsampled_R2.fastq.gz -s ${sampleId}_hostfiltered_downsampled_S.fastq.gz
+        samtools collate -u ${downsampled_bam} -o ${sampleId}.collate.bam ${sampleId}
+        samtools fastq -n -0 /dev/null -1 ${sampleId}_hostfiltered_downsampled_R1.fastq.gz -2 ${sampleId}_hostfiltered_downsampled_R2.fastq.gz -s ${sampleId}_hostfiltered_downsampled_S.fastq.gz ${sampleId}.collate.bam
         """
 }