only run clockwork is paired_end and not ont data

theiagen · Sep 21, 2023 · 57e3ef6 · 57e3ef6
1 parent 759180c
commit 57e3ef6
Showing 1 changed file with 9 additions and 7 deletions.
diff --git a/workflows/utilities/wf_merlin_magic.wdl b/workflows/utilities/wf_merlin_magic.wdl
@@ -235,16 +235,18 @@ workflow merlin_magic {
   }
   if (merlin_tag == "Mycobacterium tuberculosis") {
     if (!assembly_only) {
-      call clockwork_task.clockwork_decon_reads {
-        input:
-          read1 = select_first([read1]),
-          read2 = read2,
-          samplename = samplename
+      if (paired_end && !ont_data) {
+        call clockwork_task.clockwork_decon_reads {
+          input:
+            read1 = select_first([read1]),
+            read2 = read2,
+            samplename = samplename
+        }
       }
       call tbprofiler_task.tbprofiler {
         input:
-          read1 = clockwork_decon_reads.clockwork_cleaned_read1,
-          read2 = clockwork_decon_reads.clockwork_cleaned_read2,
+          read1 = select_first([clockwork_decon_reads.clockwork_cleaned_read1,read1]),
+          read2 = select_first([clockwork_decon_reads.clockwork_cleaned_read2,read2]),
           samplename = samplename
       }
       if (tbprofiler_additional_outputs) {