2 changed files with 16 additions and 12 deletions
+ 8
- 6
tasks/TNscope.wdl
View File
| @@ -32,13 +32,15 @@ task TNscope { | |||
| set -e | |||
| export SENTIEON_LICENSE=${SENTIEON_LICENSE} | |||
| nt=$(nproc) | |||
| mkdir -p /cromwell_root/tmp/PON/ | |||
| cp ${cosmic_dir}/${cosmic_vcf} /cromwell_root/tmp/PON/ | |||
| cp ${pon_vcf} /cromwell_root/tmp/PON/ | |||
| ${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/PON/${cosmic_vcf} | |||
| ${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/PON/$(basename ${pon_vcf}) | |||
| if ${set_pon}; then | |||
| mkdir -p /cromwell_root/tmp/PON/ | |||
| cp ${cosmic_dir}/${cosmic_vcf} /cromwell_root/tmp/PON/ | |||
| cp ${pon_vcf} /cromwell_root/tmp/PON/ | |||
| ${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/PON/${cosmic_vcf} | |||
| ${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/PON/$(basename ${pon_vcf}) | |||
| fi | |||
| if ${TN}; then | |||
| ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} -i ${corealigner_bam} --algo TNscope --tumor_sample ${tumor_name} --normal_sample ${normal_name} --dbsnp ${dbsnp_dir}/${dbsnp} ${pon_command} ${sample}.TNscope.TN.vcf | |||
| else | |||
+ 8
- 6
tasks/TNseq.wdl
View File
| @@ -31,12 +31,14 @@ task TNseq { | |||
| export SENTIEON_LICENSE=${SENTIEON_LICENSE} | |||
| nt=$(nproc) | |||
| mkdir -p /cromwell_root/tmp/PON/ | |||
| cp ${cosmic_dir}/${cosmic_vcf} /cromwell_root/tmp/PON/ | |||
| cp ${pon_vcf} /cromwell_root/tmp/PON/ | |||
| ${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/PON/${cosmic_vcf} | |||
| ${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/PON/$(basename ${pon_vcf}) | |||
| if ${set_pon}; then | |||
| mkdir -p /cromwell_root/tmp/PON/ | |||
| cp ${cosmic_dir}/${cosmic_vcf} /cromwell_root/tmp/PON/ | |||
| cp ${pon_vcf} /cromwell_root/tmp/PON/ | |||
| ${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/PON/${cosmic_vcf} | |||
| ${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/PON/$(basename ${pon_vcf}) | |||
| fi | |||
| if ${TN}; then | |||
| ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} -i ${corealigner_bam} --algo TNhaplotyper --tumor_sample ${tumor_name} --normal_sample ${normal_name} --dbsnp ${dbsnp_dir}/${dbsnp} ${pon_command} ${sample}.TNseq.TN.vcf | |||
| else | |||
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