Made finalization optional in SRBamToFq.

broadinstitute · Dec 9, 2024 · 039478c · 039478c
1 parent e46a4e2
commit 039478c
Showing 1 changed file with 11 additions and 9 deletions.
diff --git a/wdl/pipelines/TechAgnostic/Utility/SRBamToFq.wdl b/wdl/pipelines/TechAgnostic/Utility/SRBamToFq.wdl
@@ -8,20 +8,22 @@ workflow SRBamToFq {
         File bam
         String participant_name
 
-        String gcs_out_root_dir
+        String? gcs_out_root_dir
     }
 
-    String outdir = sub(gcs_out_root_dir, "/$", "") + "/SRBamToFq/~{participant_name}"
-
     call SRUtils.BamToFq { input: bam = bam, prefix = participant_name }
 
-    call FF.FinalizeToFile as FinalizeFqEnd1 { input: outdir = outdir, file = BamToFq.fq_end1 }
-    call FF.FinalizeToFile as FinalizeFqEnd2 { input: outdir = outdir, file = BamToFq.fq_end2 }
-    call FF.FinalizeToFile as FinalizeFqUnpaired { input: outdir = outdir, file = BamToFq.fq_unpaired }
+    if (defined(gcs_out_root_dir)) {
+        String outdir = sub(select_first([gcs_out_root_dir]), "/$", "") + "/SRBamToFq/~{participant_name}"
+
+        call FF.FinalizeToFile as FinalizeFqEnd1 { input: outdir = outdir, file = BamToFq.fq_end1 }
+        call FF.FinalizeToFile as FinalizeFqEnd2 { input: outdir = outdir, file = BamToFq.fq_end2 }
+        call FF.FinalizeToFile as FinalizeFqUnpaired { input: outdir = outdir, file = BamToFq.fq_unpaired }
+    }
 
     output {
-        File fq_end1 = FinalizeFqEnd1.gcs_path
-        File fq_end2 = FinalizeFqEnd2.gcs_path
-        File fq_unpaired = FinalizeFqUnpaired.gcs_path
+        File fq_end1 = select_first([FinalizeFqEnd1.gcs_path, BamToFq.fq_end1])
+        File fq_end2 = select_first([FinalizeFqEnd2.gcs_path, BamToFq.fq_end2])
+        File fq_unpaired = select_first([FinalizeFqUnpaired.gcs_path, BamToFq.fq_unpaired])
     }
 }