skip PBI

Author: SHuang-Broad

wdl/pipelines/PacBio/Utility/ProcessOnInstrumentDemuxedChunk.wdl

@@ -92,7 +92,7 @@ workflow ProcessOnInstrumentDemuxedChunk {
 
         File aligned_bam = FinalizeAlignedBam.gcs_path
         File aligned_bai = FinalizeAlignedBai.gcs_path
-        File aligned_pbi = FinalizeAlignedPbi.gcs_path
+        # File aligned_pbi = FinalizeAlignedPbi.gcs_path
 
         String movie = AlignHiFiUBAM.movie
 
@@ -141,12 +141,12 @@ workflow ProcessOnInstrumentDemuxedChunk {
 
     File aBAM = AlignHiFiUBAM.aligned_bam
     File aBAI = AlignHiFiUBAM.aligned_bai
-    File aPBI = AlignHiFiUBAM.aligned_pbi
+    # File aPBI = AlignHiFiUBAM.aligned_pbi
 
     # save
     call FF.FinalizeToFile as FinalizeAlignedBam { input: outdir = bc_specific_aln_out, file = aBAM, name = readgroup_id + '.bam' }
     call FF.FinalizeToFile as FinalizeAlignedBai { input: outdir = bc_specific_aln_out, file = aBAI, name = readgroup_id + '.bai' }
-    call FF.FinalizeToFile as FinalizeAlignedPbi { input: outdir = bc_specific_aln_out, file = aPBI, name = readgroup_id + '.pbi' }
+    # call FF.FinalizeToFile as FinalizeAlignedPbi { input: outdir = bc_specific_aln_out, file = aPBI, name = readgroup_id + '.pbi' }
 
     ###################################################################################
     # QC

wdl/tasks/Alignment/AlignHiFiUBAM.wdl

@@ -33,7 +33,7 @@ workflow AlignHiFiUBAM {
     output {
         File aligned_bam = aBAM
         File aligned_bai = aBAI
-        File aligned_pbi = IndexAlignedReads.pbi
+        # File aligned_pbi = IndexAlignedReads.pbi
 
         String movie = movie_name
         String total_runtime = select_first([sumRuntimes.total_runtime, AlignReadsTogether.wallclocktime])
@@ -103,7 +103,7 @@ workflow AlignHiFiUBAM {
 
     File aBAM = select_first([MergeAlignedReads.merged_bam, AlignReadsTogether.aligned_bam])
     File aBAI = select_first([MergeAlignedReads.merged_bai, AlignReadsTogether.aligned_bai])
-    call PB.PBIndex as IndexAlignedReads { input: bam = aBAM }
+    # call PB.PBIndex as IndexAlignedReads { input: bam = aBAM }
 }
 
 task sumRuntimes {