Merge pull request #122 from mskcc/feature/handle_empty_vcf_into_gbcms

Fix for handling handle empty vcf and maf
mskcc · Jul 13, 2023 · 59b69ee · 59b69ee
2 parents 9f7b5b5 + bd38a85
commit 59b69ee
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Showing 2 changed files with 33 additions and 4 deletions.
diff --git a/cwl/fillout_maf2vcf.cwl b/cwl/fillout_maf2vcf.cwl
@@ -26,9 +26,9 @@ requirements:
         vcf_sorted_gz="${ return inputs.sample_id + '.sorted.vcf.gz' }"
         sample_id="${ return inputs.sample_id }"
         # convert maf to vcf
-        num_lines=num_lines="\$(wc -l < \${input_maf})"
-        more_than_five="\$(( \${num_lines} > 5))"
-        if [ "\${more_than_five}" == "1" ]
+        num_lines="\$(grep -v '^[#]' \${input_maf} | wc -l)"
+        more_than_one="\$(( \${num_lines} > 1))"
+        if [ "\${more_than_one}" == "1" ]
         then
           maf2vcf.pl --output-dir . --input-maf "\${input_maf}" --output-vcf "\${vcf}" --ref-fasta "\${fasta}"
         else

diff --git a/cwl/samples_fillout_workflow.cwl b/cwl/samples_fillout_workflow.cwl
@@ -133,10 +133,39 @@ steps:
                   var args2 = args1.map( (a) => "--bam " + a )
                   return args2.join(" ") ;
                   }'
+                header_line='${
+                  var headers = ["CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT"]
+                  var sample_ids = inputs.sample_ids
+                  var header_list = headers.concat(sample_ids)
+                  return header_list.join("\t");
+                }'
                 fasta="${ return inputs.ref_fasta.path; }"
                 vcf="${ return inputs.targets_vcf.path }"
                 fillout_vcf="fillout.vcf"
-                GetBaseCountsMultiSample --fasta "\${fasta}" --vcf "\${vcf}" --maq 20 --baq 20 --filter_improper_pair 0 --thread 8 --output "\${fillout_vcf}" \${bams_arg}
+                num_lines="\$(grep -v '^[#]' \${vcf} | wc -l)"
+                more_than_zero="\$(( \${num_lines} > 0))"
+                if [ "\${more_than_zero}" == "1" ]
+                then
+                  GetBaseCountsMultiSample --fasta "\${fasta}" --vcf "\${vcf}" --maq 20 --baq 20 --filter_improper_pair 0 --thread 8 --output "\${fillout_vcf}" \${bams_arg}
+                else
+                  cat << EOF > "\${fillout_vcf}"
+                ##fileformat=VCFv4.2
+                ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total depth">
+                ##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth matching reference (REF) allele">
+                ##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth matching alternate (ALT) allele">
+                ##FORMAT=<ID=VF,Number=1,Type=Float,Description="Variant frequence (AD/DP)">
+                ##FORMAT=<ID=DPP,Number=1,Type=Integer,Description="Depth on postitive strand">
+                ##FORMAT=<ID=DPN,Number=1,Type=Integer,Description="Depth on negative strand">
+                ##FORMAT=<ID=RDP,Number=1,Type=Integer,Description="Reference depth on postitive strand">
+                ##FORMAT=<ID=RDN,Number=1,Type=Integer,Description="Reference depth on negative strand">
+                ##FORMAT=<ID=ADP,Number=1,Type=Integer,Description="Alternate depth on postitive strand">
+                ##FORMAT=<ID=ADN,Number=1,Type=Integer,Description="Alternate depth on negative strand">
+                ##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">
+                #\${header_line}
+                EOF
+                fi
       inputs:
         sample_ids: string[]
         ref_fasta: