1 changed files with 2 additions and 4 deletions
+ 2
- 4
tasks/battenberg.wdl
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| cp ${normal_bam} ./${normal_id}.bam | cp ${normal_bam} ./${normal_id}.bam | ||||
| cp ${tumor_bam} ./${sample_id}.bam | cp ${tumor_bam} ./${sample_id}.bam | ||||
| 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 | |||||
| /opt/conda/envs/batternberg/bin/samtools view -h -@ 16 -o ${normal_id}.sorted.deduped.sam ./${normal_id}.bam | |||||
| >>> | >>> | ||||
| } | } | ||||
| output { | output { | ||||
| File tumor_bam_data = "${normal_id}.sorted.deduped.sam" | |||||
| File normal_bam_data = "${sample_id}.sorted.deduped.sam" | |||||
| File normal_bam_data = "${normal_id}.sorted.deduped.sam" | |||||
| } | } | ||||
| } | } |
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