Fixed issue with the locus being fed into samtools

broadinstitute · Dec 5, 2024 · 5af47fb · 5af47fb
1 parent e40daff
commit 5af47fb
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/wdl/HidiveCorrect.wdl b/wdl/HidiveCorrect.wdl
@@ -237,8 +237,10 @@ task Consensus {
     command <<<
         set -x
 
-        samtools faidx ~{reference} ~{locus} | bcftools consensus -H 1pIu ~{calls_vcf} | minimap2 -ayYL -x map-hifi ~{reference} - | samtools sort --write-index -O BAM -o h1.bam
-        samtools faidx ~{reference} ~{locus} | bcftools consensus -H 2pIu ~{calls_vcf} | minimap2 -ayYL -x map-hifi ~{reference} - | samtools sort --write-index -O BAM -o h2.bam
+        LOCUS=$(echo "~{locus}" | sed 's/,//g' | sed 's/|.*//')
+
+        samtools faidx ~{reference} ${LOCUS} | bcftools consensus -H 1pIu ~{calls_vcf} | minimap2 -ayYL -x map-hifi ~{reference} - | samtools sort --write-index -O BAM -o h1.bam
+        samtools faidx ~{reference} ${LOCUS} | bcftools consensus -H 2pIu ~{calls_vcf} | minimap2 -ayYL -x map-hifi ~{reference} - | samtools sort --write-index -O BAM -o h2.bam
     >>>
 
     output {