Updated AnnotateIntervals task and calls in WDL (untested).

broadinstitute · Sep 7, 2018 · 73f5409 · 73f5409
1 parent 7c859e1
commit 73f5409
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diff --git a/scripts/cnv_wdl/cnv_common_tasks.wdl b/scripts/cnv_wdl/cnv_common_tasks.wdl
@@ -56,6 +56,9 @@ task AnnotateIntervals {
     File ref_fasta
     File ref_fasta_fai
     File ref_fasta_dict
+    File? mappability_track
+    File? segmental_duplication_track
+    Int? feature_query_lookahead
     File? gatk4_jar_override
 
     # Runtime parameters
@@ -76,6 +79,9 @@ task AnnotateIntervals {
         gatk --java-options "-Xmx${command_mem_mb}m" AnnotateIntervals \
             -L ${intervals} \
             --reference ${ref_fasta} \
+            ${"--mappability-track " + mappability_track} \
+            ${"--segmental-duplication-track " + segmental_duplication_track} \
+            --feature-query-lookahead ${default=1000000 feature_query_lookahead} \
             --interval-merging-rule OVERLAPPING_ONLY \
             --output annotated_intervals.tsv
     >>>

diff --git a/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl b/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl
@@ -54,6 +54,14 @@ workflow CNVGermlineCohortWorkflow {
     Int? padding
     Int? bin_length
 
+    ##################################################
+    #### optional arguments for AnnotateIntervals ####
+    ##################################################
+    File? mappability_track
+    File? segmental_duplication_track
+    Int? feature_query_lookahead
+    Int? mem_gb_for_annotate_intervals
+
     ##############################################
     #### optional arguments for CollectCounts ####
     ##############################################
@@ -146,8 +154,12 @@ workflow CNVGermlineCohortWorkflow {
                 ref_fasta = ref_fasta,
                 ref_fasta_fai = ref_fasta_fai,
                 ref_fasta_dict = ref_fasta_dict,
+                mappability_track = mappability_track,
+                segmental_duplication_track = segmental_duplication_track,
+                feature_query_lookahead = feature_query_lookahead,
                 gatk4_jar_override = gatk4_jar_override,
                 gatk_docker = gatk_docker,
+                mem_gb = mem_gb_for_annotate_intervals,
                 preemptible_attempts = preemptible_attempts
         }
     }

diff --git a/scripts/cnv_wdl/somatic/cnv_somatic_panel_workflow.wdl b/scripts/cnv_wdl/somatic/cnv_somatic_panel_workflow.wdl
@@ -58,6 +58,9 @@ workflow CNVSomaticPanelWorkflow {
     ##################################################
     #### optional arguments for AnnotateIntervals ####
     ##################################################
+    File? mappability_track
+    File? segmental_duplication_track
+    Int? feature_query_lookahead
     Int? mem_gb_for_annotate_intervals
 
     ##############################################
@@ -103,6 +106,9 @@ workflow CNVSomaticPanelWorkflow {
                 ref_fasta = ref_fasta,
                 ref_fasta_fai = ref_fasta_fai,
                 ref_fasta_dict = ref_fasta_dict,
+                mappability_track = mappability_track,
+                segmental_duplication_track = segmental_duplication_track,
+                feature_query_lookahead = feature_query_lookahead,
                 gatk4_jar_override = gatk4_jar_override,
                 gatk_docker = gatk_docker,
                 mem_gb = mem_gb_for_annotate_intervals,