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tasks/battenberg.wdl
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| @@ -18,14 +18,6 @@ task battenberg { | |||
| samtools view -h -@ 16 -o ${normal_id}.sorted.deduped.sam ./${normal_id}.bam | |||
| samtools view -h -@ 16 -o ${sample_id}.sorted.deduped.sam ./${sample_id}.bam | |||
| #sed -i 's/chr//g' ${normal_id}.sorted.deduped.sam | |||
| #sed -i 's/chr//g' ${sample_id}.sorted.deduped.sam | |||
| samtools sort -@ 16 -o ${normal_id}.sorted.deduped.nochr.bam ${normal_id}.sorted.deduped.sam | |||
| samtools sort -@ 16 -o ${sample_id}.sorted.deduped.nochr.bam ${sample_id}.sorted.deduped.sam | |||
| >>> | |||
| runtime { | |||
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