1 changed files with 8 additions and 1 deletions
+ 8
- 1
tasks/ASCAT.wdl
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| File tumor_bam_index | File tumor_bam_index | ||||
| File? normal_bam | File? normal_bam | ||||
| File? normal_bam_index | File? normal_bam_index | ||||
| File? bed_file | |||||
| String gender | String gender | ||||
| String ref_genome | String ref_genome | ||||
| String docker | String docker | ||||
| set -e | set -e | ||||
| out_dir='./' | out_dir='./' | ||||
| /root/miniconda3/envs/hrd/bin/Rscript /home/ASCAT/ascat.r ${tumor_bam} ${normal_bam} ${sample}'_T' ${sample}'_N' ${sample} WGS $out_dir ${gender} ${ref_genome} | |||||
| if [ ${bed_file} ]; then | |||||
| /root/miniconda3/envs/hrd/bin/Rscript /home/ASCAT/ascat.r ${tumor_bam} ${normal_bam} ${sample}'_T' ${sample}'_N' ${sample} WES $out_dir ${gender} ${ref_genome} ${bed_file} | |||||
| else | |||||
| /root/miniconda3/envs/hrd/bin/Rscript /home/ASCAT/ascat.r ${tumor_bam} ${normal_bam} ${sample}'_T' ${sample}'_N' ${sample} WGS $out_dir ${gender} ${ref_genome} | |||||
| fi | |||||
| ls ./ | ls ./ | ||||
| tar cvf ${sample}.tar ./ | tar cvf ${sample}.tar ./ |
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