1 fichiers modifiés avec 2 ajouts et 2 suppressions
+ 2
- 2
tasks/VEP.wdl
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| @@ -31,7 +31,7 @@ task VEP { | |||
| if [ $normal_id ]; then | |||
| SAMPLE_vcf2maf="--tumor-id $tumor_id --normal-id $normal_id" | |||
| SAMPLE_vcf2vcf="--vcf-tumor-id $tumor_id --vcf-normal-id $normal_id" | |||
| ${vcf} > raw.vcf | |||
| cp ${vcf} raw.vcf | |||
| else | |||
| SAMPLE_vcf2maf="--tumor-id $tumor_id" | |||
| # Add a column and remove it after vcf2vcf | |||
| @@ -57,7 +57,7 @@ task VEP { | |||
| --ref-fasta ${ref_dir}/${fasta} | |||
| if [ $normal_id ]; then | |||
| ${basename}.norm.vcf=norm.vcf | |||
| cp norm.vcf ${basename}.norm.vcf | |||
| else | |||
| cut -f 1,2,3,4,5,6,7,8,9,10 norm.vcf > ${basename}.norm.vcf | |||
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