Added sample ids to the vcf

mskcc · Jul 12, 2023 · 0264442 · 0264442
1 parent a58679b
commit 0264442
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/cwl/samples_fillout_workflow.cwl b/cwl/samples_fillout_workflow.cwl
@@ -133,6 +133,7 @@ steps:
                   var args2 = args1.map( (a) => "--bam " + a )
                   return args2.join(" ") ;
                   }'
+                sample_ids="${ return inputs.sample_ids.join("\t"); }"
                 fasta="${ return inputs.ref_fasta.path; }"
                 vcf="${ return inputs.targets_vcf.path }"
                 fillout_vcf="fillout.vcf"
@@ -157,7 +158,7 @@ steps:
                 ##FORMAT=<ID=DPF,Number=1,Type=Integer,Description="Total fragment depth">
                 ##FORMAT=<ID=RDF,Number=1,Type=Float,Description="Fragment depth matching reference (REF) allele">
                 ##FORMAT=<ID=ADF,Number=1,Type=Float,Description="Fragment depth matching alternate (ALT) allele">
-                #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  P-\${sample_id}       \${sample_id}
+                #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  P-\${sample_ids}
                 EOF
                 fi
       inputs: