@@ -1,7 +1,7 @@ | |||
task samtools { | |||
File bam_file | |||
String bam_id=basename(bam_file) | |||
String sample_id | |||
String docker | |||
String cluster | |||
String disk_size | |||
@@ -10,9 +10,10 @@ task samtools { | |||
command <<< | |||
set -o pipefail | |||
set -e | |||
cp ${bam_file} ${bam_id} | |||
samtools index ${bam_file} | |||
mkdir -p ${sample_id}/data | |||
cp ${bam_file} ${sample_id}/data/${bam_id} | |||
samtools index ${sample_id}/data/${bam_id} | |||
>>> | |||