Added Funcotator excluded fields option explicitly to the M2 WDLs. (#…

…5242) - M2 WDL has explicit optional parameter for a list of fields that should be excluded from the output. - Both M2 WDL files are updated. Manually tested mutect2.wdl on local backend. Closes #5141
broadinstitute · Oct 3, 2018 · e52a2d8 · e52a2d8
1 parent 26d5d7d
commit e52a2d8
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Showing 3 changed files with 17 additions and 5 deletions.
diff --git a/scripts/mutect2_wdl/mutect2.wdl b/scripts/mutect2_wdl/mutect2.wdl
@@ -57,6 +57,7 @@
 ## funco_data_sources_tar_gz:  Funcotator datasources tar gz file.  Bucket location is recommended when running on the cloud.
 ## funco_annotation_defaults:  Default values for annotations, when values are unspecified.  Specified as  <ANNOTATION>:<VALUE>.  For example:  "Center:Broad"
 ## funco_annotation_overrides:  Values for annotations, even when values are unspecified.  Specified as  <ANNOTATION>:<VALUE>.  For example:  "Center:Broad"
+## funcotator_excluded_fields:  Annotations that should not appear in the output (VCF or MAF).  Specified as  <ANNOTATION>.  For example:  "ClinVar_ALLELEID"
 ##
 ## Outputs :
 ## - One VCF file and its index with primary filtering applied; secondary filtering and functional annotation if requested; a bamout.bam
@@ -116,6 +117,7 @@ workflow Mutect2 {
     String? sequencing_center
     String? sequence_source
     File? default_config_file
+    String? oncotator_extra_args
 
     # funcotator inputs
     Boolean? run_funcotator
@@ -126,6 +128,8 @@ workflow Mutect2 {
     File? funco_transcript_selection_list
     Array[String]? funco_annotation_defaults
     Array[String]? funco_annotation_overrides
+    Array[String]? funcotator_excluded_fields
+    String? funcotator_extra_args
 
     File? gatk_override
 
@@ -138,8 +142,6 @@ workflow Mutect2 {
     Boolean filter_oncotator_maf_or_default = select_first([filter_oncotator_maf, true])
     Boolean? filter_funcotations
     Boolean filter_funcotations_or_default = select_first([filter_funcotations, true])
-    String? oncotator_extra_args
-    String? funcotator_extra_args
 
     Int? preemptible_attempts
     Int? max_retries
@@ -429,6 +431,7 @@ workflow Mutect2 {
                 gatk_docker = gatk_docker,
                 gatk_override = gatk_override,
                 filter_funcotations = filter_funcotations_or_default,
+                funcotator_excluded_fields = funcotator_excluded_fields,
                 sequencing_center = sequencing_center,
                 sequence_source = sequence_source,
                 disk_space_gb = ceil(size(funcotate_vcf_input, "GB") * large_input_to_output_multiplier) + onco_tar_size + disk_pad,
@@ -1197,6 +1200,7 @@ task FuncotateMaf {
      File? transcript_selection_list
      Array[String]? annotation_defaults
      Array[String]? annotation_overrides
+     Array[String]? funcotator_excluded_fields
      Boolean filter_funcotations
      File? interval_list
 
@@ -1207,6 +1211,7 @@ task FuncotateMaf {
      String annotation_def_arg = if defined(annotation_defaults) then " --annotation-default " else ""
      String annotation_over_arg = if defined(annotation_overrides) then " --annotation-override " else ""
      String filter_funcotations_args = if (filter_funcotations) then " --remove-filtered-variants " else ""
+     String excluded_fields_args = if defined(funcotator_excluded_fields) then " --exclude-field " else ""
      String final_output_filename = basename(input_vcf, ".vcf") + ".maf.annotated"
      # ==============
 
@@ -1269,6 +1274,7 @@ task FuncotateMaf {
             --annotation-default source:${default="Unknown" sequence_source} \
              ${annotation_def_arg}${default="" sep=" --annotation-default " annotation_defaults} \
              ${annotation_over_arg}${default="" sep=" --annotation-override " annotation_overrides} \
+             ${excluded_fields_args}${default="" sep=" --exclude-field " funcotator_excluded_fields} \
              ${filter_funcotations_args} \
              ${extra_args}
      >>>

diff --git a/scripts/mutect2_wdl/mutect2_nio.wdl b/scripts/mutect2_wdl/mutect2_nio.wdl
@@ -55,6 +55,7 @@
 ## funco_data_sources_tar_gz:  Funcotator datasources tar gz file.  Bucket location is recommended when running on the cloud.
 ## funco_annotation_defaults:  Default values for annotations, when values are unspecified.  Specified as  <ANNOTATION>:<VALUE>.  For example:  "Center:Broad"
 ## funco_annotation_overrides:  Values for annotations, even when values are unspecified.  Specified as  <ANNOTATION>:<VALUE>.  For example:  "Center:Broad"
+## funcotator_excluded_fields:  Annotations that should not appear in the output (VCF or MAF).  Specified as  <ANNOTATION>.  For example:  "ClinVar_ALLELEID"
 ##
 ## Outputs :
 ## - One VCF file and its index with primary filtering applied; secondary filtering and functional annotation if requested; a bamout.bam
@@ -107,6 +108,7 @@ workflow Mutect2 {
     String? sequencing_center
     String? sequence_source
     File? default_config_file
+    String? oncotator_extra_args
 
     # funcotator inputs
     Boolean? run_funcotator
@@ -117,6 +119,8 @@ workflow Mutect2 {
     File? funco_transcript_selection_list
     Array[String]? funco_annotation_defaults
     Array[String]? funco_annotation_overrides
+    Array[String]? funcotator_excluded_fields
+    String? funcotator_extra_args
 
     File? gatk_override
 
@@ -129,8 +133,6 @@ workflow Mutect2 {
     Boolean filter_oncotator_maf_or_default = select_first([filter_oncotator_maf, true])
     Boolean? filter_funcotations
     Boolean filter_funcotations_or_default = select_first([filter_funcotations, true])
-    String? oncotator_extra_args
-    String? funcotator_extra_args
 
     Int? preemptible_attempts
     Int? max_retries
@@ -373,6 +375,7 @@ workflow Mutect2 {
                 gatk_docker = gatk_docker,
                 gatk_override = gatk_override,
                 filter_funcotations = filter_funcotations_or_default,
+                funcotator_excluded_fields = funcotator_excluded_fields,
                 sequencing_center = sequencing_center,
                 sequence_source = sequence_source,
                 disk_space_gb = ceil(size(funcotate_vcf_input, "GB") * large_input_to_output_multiplier) + funco_tar_size + disk_pad,
@@ -1013,6 +1016,7 @@ task FuncotateMaf {
      File? transcript_selection_list
      Array[String]? annotation_defaults
      Array[String]? annotation_overrides
+     Array[String]? funcotator_excluded_fields
      Boolean filter_funcotations
      File? interval_list
 
@@ -1023,6 +1027,7 @@ task FuncotateMaf {
      String annotation_def_arg = if defined(annotation_defaults) then " --annotation-default " else ""
      String annotation_over_arg = if defined(annotation_overrides) then " --annotation-override " else ""
      String filter_funcotations_args = if (filter_funcotations) then " --remove-filtered-variants " else ""
+     String excluded_fields_args = if defined(funcotator_excluded_fields) then " --exclude-field " else ""
      String final_output_filename = basename(input_vcf, ".vcf") + ".maf.annotated"
      # ==============
 
@@ -1085,6 +1090,7 @@ task FuncotateMaf {
             --annotation-default source:${default="Unknown" sequence_source} \
              ${annotation_def_arg}${default="" sep=" --annotation-default " annotation_defaults} \
              ${annotation_over_arg}${default="" sep=" --annotation-override " annotation_overrides} \
+             ${excluded_fields_args}${default="" sep=" --exclude-field " funcotator_excluded_fields} \
              ${filter_funcotations_args} \
              ${extra_args}
      >>>

diff --git a/scripts/mutect2_wdl/unsupported/funcotator.wdl b/scripts/mutect2_wdl/unsupported/funcotator.wdl
@@ -20,7 +20,7 @@
 #     annotation_defaults            -  Annotations to include in all annotated variants if the annotation is not specified in the data sources (in the format <ANNOTATION>:<VALUE>).  This will add the specified annotation to every annotated variant if it is not already present.
 #     annotation_overrides           -  Override values for annotations (in the format <ANNOTATION>:<VALUE>).  Replaces existing annotations of the given name with given values.
 #     gatk4_jar_override             -  Override Jar file containing GATK 4.0.  Use this when overriding the docker JAR or when using a backend without docker.
-#     funcotator_extra_args          -  Extra command-line arguments to pass through to Funcotator.
+#     funcotator_extra_args          -  Extra command-line arguments to pass through to Funcotator.  (e.g. " --exclude-field foo_field --exclude-field bar_field ")
 #
 # This WDL needs to decide whether to use the ``gatk_jar`` or ``gatk_jar_override`` for the jar location.  As of cromwell-0.24,
 # this logic *must* go into each task.  Therefore, there is a lot of duplicated code.  This allows users to specify a jar file