Exposed ability to blacklist intervals in CNV WDLs.

broadinstitute · Jul 18, 2018 · 4c3524e · 4c3524e
1 parent 1977c53
commit 4c3524e
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Showing 5 changed files with 11 additions and 1 deletion.
diff --git a/scripts/cnv_wdl/cnv_common_tasks.wdl b/scripts/cnv_wdl/cnv_common_tasks.wdl
@@ -1,5 +1,6 @@
 task PreprocessIntervals {
     File? intervals
+    File? blacklist_intervals
     File ref_fasta
     File ref_fasta_fai
     File ref_fasta_dict
@@ -28,6 +29,7 @@ task PreprocessIntervals {
 
         gatk --java-options "-Xmx${command_mem_mb}m" PreprocessIntervals \
             ${"-L " + intervals} \
+            ${"-XL " + blacklist_intervals} \
             --sequence-dictionary ${ref_fasta_dict} \
             --reference ${ref_fasta} \
             --padding ${default="250" padding} \

diff --git a/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl b/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl
@@ -21,6 +21,7 @@ workflow CNVGermlineCaseWorkflow {
     #### required basic arguments ####
     ##################################
     File intervals
+    File? blacklist_intervals
     File bam
     File bam_idx
     File contig_ploidy_model_tar
@@ -98,6 +99,7 @@ workflow CNVGermlineCaseWorkflow {
     call CNVTasks.PreprocessIntervals {
         input:
             intervals = intervals,
+            blacklist_intervals = blacklist_intervals,
             ref_fasta = ref_fasta,
             ref_fasta_fai = ref_fasta_fai,
             ref_fasta_dict = ref_fasta_dict,

diff --git a/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl b/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl
@@ -21,6 +21,7 @@ workflow CNVGermlineCohortWorkflow {
     #### required basic arguments ####
     ##################################
     File intervals
+    File? blacklist_intervals
     Array[String] normal_bams
     Array[String] normal_bais
     String cohort_entity_id
@@ -120,6 +121,7 @@ workflow CNVGermlineCohortWorkflow {
     call CNVTasks.PreprocessIntervals {
         input:
             intervals = intervals,
+            blacklist_intervals = blacklist_intervals,
             ref_fasta = ref_fasta,
             ref_fasta_fai = ref_fasta_fai,
             ref_fasta_dict = ref_fasta_dict,

diff --git a/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl b/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl
@@ -28,6 +28,7 @@ workflow CNVSomaticPairWorkflow {
     ##################################
     File common_sites
     File intervals
+    File? blacklist_intervals
     File tumor_bam
     File tumor_bam_idx
     File? normal_bam
@@ -126,7 +127,7 @@ workflow CNVSomaticPairWorkflow {
 
     Int gatk4_override_size = if defined(gatk4_jar_override) then ceil(size(gatk4_jar_override, "GB")) else 0
     # This is added to every task as padding, should increase if systematically you need more disk for every call
-    Int disk_pad = 20 + ceil(size(intervals, "GB")) + ceil(size(common_sites, "GB")) + gatk4_override_size + select_first([emergency_extra_disk,0])
+    Int disk_pad = 20 + ceil(size(intervals, "GB")) + ceil(size(common_sites, "GB")) + gatk4_override_size + select_first([emergency_extra_disk, 0])
 
     File final_normal_bam = select_first([normal_bam, "null"])
     File final_normal_bam_idx = select_first([normal_bam_idx, "null"])
@@ -135,6 +136,7 @@ workflow CNVSomaticPairWorkflow {
     call CNVTasks.PreprocessIntervals {
         input:
             intervals = intervals,
+            blacklist_intervals = blacklist_intervals,
             ref_fasta = ref_fasta,
             ref_fasta_fai = ref_fasta_fai,
             ref_fasta_dict = ref_fasta_dict,

diff --git a/scripts/cnv_wdl/somatic/cnv_somatic_panel_workflow.wdl b/scripts/cnv_wdl/somatic/cnv_somatic_panel_workflow.wdl
@@ -23,6 +23,7 @@ workflow CNVSomaticPanelWorkflow {
     #### required basic arguments ####
     ##################################
     File intervals
+    File? blacklist_intervals
     Array[String] normal_bams
     Array[String] normal_bais
     String pon_entity_id
@@ -76,6 +77,7 @@ workflow CNVSomaticPanelWorkflow {
     call CNVTasks.PreprocessIntervals {
         input:
             intervals = intervals,
+            blacklist_intervals = blacklist_intervals,
             ref_fasta = ref_fasta,
             ref_fasta_fai = ref_fasta_fai,
             ref_fasta_dict = ref_fasta_dict,