fix(wdl): Enable SAM output for minimap2

broadinstitute · Jan 9, 2025 · 1252566 · 1252566
1 parent f0278e2
commit 1252566
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/wdl/tasks/alignment/minimap2.wdl b/wdl/tasks/alignment/minimap2.wdl
@@ -97,7 +97,7 @@ task Minimap2WithIx {
     
     command <<<
         set -euxo pipefail
-        minimap2 -t ~{num_cpu - 1} ~{extra_params} -d ~{ref_mmi} ~{query_fasta} \
+        minimap2 -t ~{num_cpu - 1} ~{extra_params} -a -d ~{ref_mmi} ~{query_fasta} \
             | samtools sort -Obam -o ~{out_prefix}.bam
     >>>