2 changed files with 2 additions and 2 deletions
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tasks/MSIsensor.wdl
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| # MSI | # MSI | ||||
| mkdir -p /cromwell_root/tmp/${sample} | mkdir -p /cromwell_root/tmp/${sample} | ||||
| msisensor-pro scan -d ${ref_dir}/${fasta} -o reference.list | msisensor-pro scan -d ${ref_dir}/${fasta} -o reference.list | ||||
| if [ ${normal_recaled_bam} ]; then | |||||
| if [ ${normal_bam} ]; then | |||||
| msisensor-pro msi -d reference.list -n ${normal_bam} -t ${tumor_bam} -o /cromwell_root/tmp/${sample} | msisensor-pro msi -d reference.list -n ${normal_bam} -t ${tumor_bam} -o /cromwell_root/tmp/${sample} | ||||
| else | else | ||||
| msisensor-pro pro -d ${baseline} -t ${tumor_bam} -o /cromwell_root/tmp/${sample} | msisensor-pro pro -d ${baseline} -t ${tumor_bam} -o /cromwell_root/tmp/${sample} |
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workflow.wdl
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| cluster_config=cluster_config, | cluster_config=cluster_config, | ||||
| disk_size=disk_size | disk_size=disk_size | ||||
| } | } | ||||
| call CNVkit.CNVkit as CNVkit { | call CNVkit.CNVkit as CNVkit { | ||||
| input: | input: | ||||
| sample=sample_id, | sample=sample_id, |
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