2 changed files with 4 additions and 4 deletions
+ 3
- 3
tasks/fastq_ncm.wdl
View File
| File fq1 | File fq1 | ||||
| File fq2 | File fq2 | ||||
| String output_id | |||||
| String out_id | |||||
| String subsampling_rate | String subsampling_rate | ||||
| String docker | String docker | ||||
| String cluster_config | String cluster_config | ||||
| set -e | set -e | ||||
| nt=$(nproc) | nt=$(nproc) | ||||
| export NCM_HOME=/opt/NGSCheckMate | export NCM_HOME=/opt/NGSCheckMate | ||||
| /opt/NGSCheckMate/ngscheckmate_fastq -1 ${fq1} -2 ${fq2} /opt/NGSCheckMate/SNP/SNP.pt -p $nt -s ${subsampling_rate} > ${output_id}.vaf | |||||
| /opt/NGSCheckMate/ngscheckmate_fastq -1 ${fq1} -2 ${fq2} /opt/NGSCheckMate/SNP/SNP.pt -p $nt -s ${subsampling_rate} > ${out_id}.vaf | |||||
| >>> | >>> | ||||
| runtime { | runtime { | ||||
| dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/" | dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/" | ||||
| } | } | ||||
| output { | output { | ||||
| File vaf="${output_id}.vaf" | |||||
| File vaf="${out_id}.vaf" | |||||
| } | } | ||||
| } | } |
+ 1
- 1
workflow.wdl
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| input: | input: | ||||
| fq1=fastq1[idx], | fq1=fastq1[idx], | ||||
| fq2=fastq2[idx], | fq2=fastq2[idx], | ||||
| output_id=output_id[idx], | |||||
| out_id=output_id[idx], | |||||
| subsampling_rate=subsampling_rate, | subsampling_rate=subsampling_rate, | ||||
| docker=docker, | docker=docker, | ||||
| disk_size=disk_size, | disk_size=disk_size, |
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