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tasks/prepareaa.wdl
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| command <<< | command <<< | ||||
| set -o pipefail | set -o pipefail | ||||
| set -e | set -e | ||||
| cd /home/input | |||||
| cp ${dedup_bam} ./ | |||||
| cp ${dedup_bamindex} ./ | |||||
| /home/programs/PrepareAA-master/PrepareAA.py -s ${sample_name} -t 15 --cnvkit_dir /home/programs/cnvkit.py --sorted_bam /home/input/${dedup_bam} --run_AA --ref GRCh38 -o /home/output | /home/programs/PrepareAA-master/PrepareAA.py -s ${sample_name} -t 15 --cnvkit_dir /home/programs/cnvkit.py --sorted_bam /home/input/${dedup_bam} --run_AA --ref GRCh38 -o /home/output | ||||
| >>> | >>> |
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