one sequencing facility changed how they run primrose, we change strategy

Author: SHuang-Broad

wdl/pipelines/PacBio/Utility/SplitMergedPacBioBamByReadgroup.wdl

@@ -17,6 +17,7 @@ workflow SplitMergedPacBioBamByReadgroup {
 
         Boolean unmap_bam
         Boolean convert_to_fq = false
+        Boolean disable_primrose_check = false
 
         String gcs_out_root_dir
     }
@@ -37,6 +38,7 @@ workflow SplitMergedPacBioBamByReadgroup {
         platform:  "long reads platform the BAM was generated on; must be one of [PB, ONT]"
         convert_to_fq: "user option to convert to FASTQ (gz) or not"
         gcs_out_root_dir: "place to store the result files"
+        disable_primrose_check: "when true, disable a QC check making sure primrose is run on all readgroups; only do this when you know what you're doing"
     }
 
     ##############################################################################################################################
@@ -49,9 +51,11 @@ workflow SplitMergedPacBioBamByReadgroup {
     }
 
     # this guarantees that there are no read groups missing primrose runs
-    call PBUtils.VerifyPacBioBamHasAppropriatePrimroseRuns as PrimroseCheck { input: bam = input_bam }
-    if (0!= length(PrimroseCheck.readgroups_missing_primrose)) {
-        call Utils.StopWorkflow as MissingPrimrose { input: reason = "Input BAM file has some of its read groups missing primrose calls."}
+    if (!disable_primrose_check) {
+        call PBUtils.VerifyPacBioBamHasAppropriatePrimroseRuns as PrimroseCheck { input: bam = input_bam }
+        if (0!= length(PrimroseCheck.readgroups_missing_primrose)) {
+            call Utils.StopWorkflow as MissingPrimrose { input: reason = "Input BAM file has some of its read groups missing primrose calls."}
+        }
     }
 
     # delegate