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command <<< |
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command <<< |
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set -o pipefail |
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set -o pipefail |
|
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set -e |
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set -e |
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bamdst -p ${bed} -o ./ ${bam} |
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mkdir -p /cromwell_root/tmp/bamdst |
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bamdst -p ${bed} -o /cromwell_root/tmp/bamdst ${bam} |
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|
|
cd /cromwell_root/tmp/bamdst |
|
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cp chromosomes.report ${sample}_chromosomes.report |
|
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cp chromosomes.report ${sample}_chromosomes.report |
|
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cp coverage.report ${sample}_coverage.report |
|
|
cp coverage.report ${sample}_coverage.report |
|
|
cp depth_distribution.plot ${sample}_depth_distribution.plot |
|
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cp depth_distribution.plot ${sample}_depth_distribution.plot |