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tasks/fusioncatcher.wdl
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| set -o pipefail | set -o pipefail | ||||
| set -e | set -e | ||||
| mkdir -p /cromwell_root/${sample_id}/input/ | |||||
| mkdir -p /cromwell_root/${sample_id}/output/ | |||||
| cp ${fastq1} /cromwell_root/${sample_id}/input/ | |||||
| cp ${fastq2} /cromwell_root/${sample_id}/input/ | |||||
| mkdir -p /cromwell_root/input/ | |||||
| mkdir -p /cromwell_root/output/ | |||||
| cp ${fastq1} /cromwell_root/input/ | |||||
| cp ${fastq2} /cromwell_root/input/ | |||||
| /software/fusioncatcher/bin/fusioncatcher \ | /software/fusioncatcher/bin/fusioncatcher \ | ||||
| -d ${database_dir} \ | -d ${database_dir} \ | ||||
| -p 4 \ | -p 4 \ | ||||
| --input /cromwell_root/${sample_id}/input \ | |||||
| --output /cromwell_root/${sample_id}/output | |||||
| --input /cromwell_root/input \ | |||||
| --output /cromwell_root/output | |||||
| >>> | >>> | ||||
| } | } | ||||
| output { | output { | ||||
| Array[File] fusioncatcher_result=glob("/cromwell_root/${sample_id}/output/*.txt") | |||||
| Array[File] fusioncatcher_zip=glob("/cromwell_root/${sample_id}/output/*.zip") | |||||
| Array[File] fusioncatcher_log=glob("/cromwell_root/${sample_id}/output/*.log") | |||||
| Array[File] fusioncatcher_vcf=glob("/cromwell_root/${sample_id}/output/*.vcf") | |||||
| Array[File] fusioncatcher_result=glob("/cromwell_root/output/*.txt") | |||||
| Array[File] fusioncatcher_zip=glob("/cromwell_root/output/*.zip") | |||||
| Array[File] fusioncatcher_log=glob("/cromwell_root/output/*.log") | |||||
| Array[File] fusioncatcher_vcf=glob("/cromwell_root/output/*.vcf") | |||||
| } | } | ||||
| } | } |
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