adding support for vcf files named in the format: ${chr}.dose*vcf.gz

anand-imcm · Jul 26, 2024 · e20013b · e20013b
1 parent 2ccb9b0
commit e20013b
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/workflows/tasks/extract_info.wdl b/workflows/tasks/extract_info.wdl
@@ -32,9 +32,9 @@ task extract {
             awk -v chr=$chr '$1 == chr' ~{query_variants} > ${chr}_query_subset_variants_list.txt
             if [ -f ${chr}_query_subset_variants_list.txt ]; then
                 if [ -n "~{query_samples}" ] && [ -f ~{query_samples} ]; then
-                    bcftools view --regions-file ${chr}_query_subset_variants_list.txt --samples-file ~{query_samples} ${chr}.dose.vcf.gz > ~{prefix}_${chr}_query_subset.vcf
+                    bcftools view --regions-file ${chr}_query_subset_variants_list.txt --samples-file ~{query_samples} ${chr}.dose*vcf.gz > ~{prefix}_${chr}_query_subset.vcf
                 else
-                    bcftools view --regions-file ${chr}_query_subset_variants_list.txt ${chr}.dose.vcf.gz > ~{prefix}_${chr}_query_subset.vcf
+                    bcftools view --regions-file ${chr}_query_subset_variants_list.txt ${chr}.dose*vcf.gz > ~{prefix}_${chr}_query_subset.vcf
                 fi
                 if [ "~{match_pos_only}" = "false" ]; then
                     python3 /scripts/filter_vcf.py --query ${chr}_query_subset_variants_list.txt --vcf ~{prefix}_${chr}_query_subset.vcf --out ~{prefix}_${chr}_query_matched_alleles_subset