1 changed files with 2 additions and 1 deletions
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tasks/TNscope.wdl
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| -i ${tumor_bam} -q ${tumor_recall_data} \ | -i ${tumor_bam} -q ${tumor_recall_data} \ | ||||
| -i ${normal_bam} -q ${normal_recall_data} \ | -i ${normal_bam} -q ${normal_recall_data} \ | ||||
| --algo TNscope --tumor_sample ${tumor_name} --normal_sample ${normal_name} \ | --algo TNscope --tumor_sample ${tumor_name} --normal_sample ${normal_name} \ | ||||
| --disable_detector sv --trim_soft_clip \ | |||||
| --trim_soft_clip \ | |||||
| --dbsnp ${dbsnp_dir}/${dbsnp} ${sample_id}.TNscope.vcf || { echo "TNscope failed"; exit 1; } | --dbsnp ${dbsnp_dir}/${dbsnp} ${sample_id}.TNscope.vcf || { echo "TNscope failed"; exit 1; } | ||||
| ls ./ | ls ./ | ||||
| #--disable_detector sv | |||||
| >>> | >>> | ||||
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