Add a readgroup flag to minimap2

biowdl · Dec 13, 2024 · 74a5e12 · 74a5e12
1 parent 98d9e2c
commit 74a5e12
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/minimap2.wdl b/minimap2.wdl
@@ -101,6 +101,7 @@ task Mapping {
         Int? matchingScore
         Int? mismatchPenalty
         String? howToFindGTAG
+        String? readgroup
 
         Int cores = 8
         String memory = "24GiB"
@@ -126,6 +127,7 @@ task Mapping {
         ~{"-A " + matchingScore} \
         ~{"-B " + mismatchPenalty} \
         ~{"-u " + howToFindGTAG} \
+        ~{"-R '" + readgroup}{false="" true="'" defined(readgroup)} \
         ~{referenceFile} \
         ~{queryFile} \
         | samtools sort \