Make LocalizeReads Optional in GatherSampleEvidence (#620)

* Added boolean variable to GatherSampleEvidence to indicate if LocalizeReads should be run with default value of true; if false, the task will be skipped. * Removed redundant implementation of localized reads in GatherSampleEvidence.wdl * Updated GatherSampleEvidence rb.CramToBamReviseBase to use input cram/bam from LocalizeReads if itis called only * Updated GatherSampleEvidence rb.CramToBamReviseBase to use input cram/bam from LocalizeReads if itis called only * Fixed the file to check for revise_bam, localize reads, and then uses the original file * Changed location of variable and input to better flow with current wdl formatting
broadinstitute · Dec 14, 2023 · dc92e9f · dc92e9f
1 parent 7607a32
commit dc92e9f
Show file tree

Hide file tree

Showing 2 changed files with 18 additions and 5 deletions.
diff --git a/wdl/GatherSampleEvidence.wdl b/wdl/GatherSampleEvidence.wdl
@@ -37,6 +37,10 @@ workflow GatherSampleEvidence {
     # Only use if encountering errors (expensive!)
     Boolean revise_base = false
 
+    # Localize reads parameters
+    # set to true on default, skips localize_reads if set to false
+    Boolean run_localize_reads = true
+
     # Common parameters
     File primary_contigs_list
     File reference_fasta
@@ -128,19 +132,22 @@ workflow GatherSampleEvidence {
   File bam_or_cram_index_ = select_first([bam_or_cram_index, bam_or_cram_file + index_ext_])
 
   # move the reads nearby -- handles requester_pays and makes cross-region transfers just once
-  call LocalizeReads {
+  if (run_localize_reads) {
+    call LocalizeReads {
     input:
       reads_path = bam_or_cram_file,
       reads_index = bam_or_cram_index_,
       move_files = move_bam_or_cram_files,
       runtime_attr_override = runtime_attr_localize_reads
+    }
   }
 
+
   if (revise_base) {
     call rb.CramToBamReviseBase {
       input:
-        cram_file = LocalizeReads.output_file,
-        cram_index = LocalizeReads.output_index,
+        cram_file = select_first([LocalizeReads.output_file, bam_or_cram_file]),
+        cram_index = select_first([LocalizeReads.output_index, bam_or_cram_index]),
         reference_fasta = reference_fasta,
         reference_index = reference_index,
         contiglist = select_first([primary_contigs_fai]),
@@ -151,8 +158,8 @@ workflow GatherSampleEvidence {
     }
   }
 
-  File reads_file_ = select_first([CramToBamReviseBase.bam_file, LocalizeReads.output_file])
-  File reads_index_ = select_first([CramToBamReviseBase.bam_index, LocalizeReads.output_index])
+  File reads_file_ = select_first([CramToBamReviseBase.bam_file, LocalizeReads.output_file, bam_or_cram_file])
+  File reads_index_ = select_first([CramToBamReviseBase.bam_index, LocalizeReads.output_index, bam_or_cram_index])
 
   if (collect_coverage || run_melt) {
     call cov.CollectCounts {
@@ -315,6 +322,7 @@ workflow GatherSampleEvidence {
   }
 }
 
+
 task LocalizeReads {
   input {
     File reads_path

diff --git a/wdl/GatherSampleEvidenceBatch.wdl b/wdl/GatherSampleEvidenceBatch.wdl
@@ -15,6 +15,10 @@ workflow GatherSampleEvidenceBatch {
     Boolean collect_coverage = true
     Boolean collect_pesr = true
 
+    # Localize reads parameters
+    # set to true on default, skips localize_reads if set to false
+    Boolean run_localize_reads = true
+
     # Common parameters
     File primary_contigs_list
     File reference_fasta
@@ -136,6 +140,7 @@ workflow GatherSampleEvidenceBatch {
         baseline_melt_vcf = baseline_melt_vcf,
         baseline_scramble_vcf = baseline_scramble_vcf,
         baseline_wham_vcf = baseline_wham_vcf,
+        run_localize_reads = run_localize_reads,
         sv_pipeline_docker = sv_pipeline_docker,
         sv_base_mini_docker = sv_base_mini_docker,
         samtools_cloud_docker = samtools_cloud_docker,