1 changed files with 3 additions and 2 deletions
+ 3
- 2
tasks/replaceRG.wdl
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| @@ -10,8 +10,9 @@ task replaceRG { | |||
| String disk_size | |||
| command <<< | |||
| samtools addreplacerg -r "@RG\tID:${group}\tSM:${sample}\tPL:${pl}" -o ${bam_name}.bam ${bam} | |||
| samtools index ${bam_name}.bam | |||
| SAMTOOLS_DIR="/opt/samtools/samtools-1.13" | |||
| $SAMTOOLS_DIR/samtools addreplacerg -r "@RG\tID:${group}\tSM:${sample}\tPL:${pl}" -o ${bam_name}.bam ${bam} | |||
| $SAMTOOLS_DIR/samtools index ${bam_name}.bam | |||
| >>> | |||
| runtime { | |||
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