Added requester pays option to Mutect2 tasks that access bams (#6879)

* Added requester pays option to Mutect2 tasks that access bams

* gnomAD isn't going to be requester pays, so we don't need that arg in
the CreatePanel task

scripts/mutect2_wdl/mutect2.wdl

@@ -108,6 +108,7 @@ workflow Mutect2 {
       Boolean? compress_vcfs
       File? gga_vcf
       File? gga_vcf_idx
+      String? gcs_project_for_requester_pays
 
       # Funcotator inputs
       Boolean? run_funcotator
@@ -271,7 +272,8 @@ workflow Mutect2 {
                 gga_vcf_idx = gga_vcf_idx,
                 gatk_override = gatk_override,
                 gatk_docker = gatk_docker,
-                disk_space = m2_per_scatter_size
+                disk_space = m2_per_scatter_size,
+                gcs_project_for_requester_pays = gcs_project_for_requester_pays
         }
     }
 
@@ -372,7 +374,8 @@ workflow Mutect2 {
                 input_vcf = Filter.filtered_vcf,
                 input_vcf_idx = Filter.filtered_vcf_idx,
                 runtime_params = standard_runtime,
-                mem = filter_alignment_artifacts_mem
+                mem = filter_alignment_artifacts_mem,
+                gcs_project_for_requester_pays = gcs_project_for_requester_pays
         }
     }
 
@@ -531,6 +534,8 @@ task M2 {
 
       File? gatk_override
 
+      String? gcs_project_for_requester_pays
+
       # runtime
       String gatk_docker
       Int? mem
@@ -579,11 +584,13 @@ task M2 {
         touch f1r2.tar.gz
         echo "" > normal_name.txt
 
-        gatk --java-options "-Xmx~{command_mem}m" GetSampleName -R ~{ref_fasta} -I ~{tumor_bam} -O tumor_name.txt -encode
+        gatk --java-options "-Xmx~{command_mem}m" GetSampleName -R ~{ref_fasta} -I ~{tumor_bam} -O tumor_name.txt -encode \
+        ~{"--gcs-project-for-requester-pays " + gcs_project_for_requester_pays}
         tumor_command_line="-I ~{tumor_bam} -tumor `cat tumor_name.txt`"
 
         if [[ ! -z "~{normal_bam}" ]]; then
-            gatk --java-options "-Xmx~{command_mem}m" GetSampleName -R ~{ref_fasta} -I ~{normal_bam} -O normal_name.txt -encode
+            gatk --java-options "-Xmx~{command_mem}m" GetSampleName -R ~{ref_fasta} -I ~{normal_bam} -O normal_name.txt -encode \
+            ~{"--gcs-project-for-requester-pays " + gcs_project_for_requester_pays}
             normal_command_line="-I ~{normal_bam} -normal `cat normal_name.txt`"
         fi
 
@@ -598,7 +605,8 @@ task M2 {
             -O "~{output_vcf}" \
             ~{true='--bam-output bamout.bam' false='' make_bamout} \
             ~{true='--f1r2-tar-gz f1r2.tar.gz' false='' run_ob_filter} \
-            ~{m2_extra_args}
+            ~{m2_extra_args} \
+            ~{"--gcs-project-for-requester-pays " + gcs_project_for_requester_pays}
 
         m2_exit_code=$?
 
@@ -612,12 +620,14 @@ task M2 {
 
         if [[ ! -z "~{variants_for_contamination}" ]]; then
             gatk --java-options "-Xmx~{command_mem}m" GetPileupSummaries -R ~{ref_fasta} -I ~{tumor_bam} ~{"--interval-set-rule INTERSECTION -L " + intervals} \
-                -V ~{variants_for_contamination} -L ~{variants_for_contamination} -O tumor-pileups.table ~{getpileupsummaries_extra_args}
+                -V ~{variants_for_contamination} -L ~{variants_for_contamination} -O tumor-pileups.table ~{getpileupsummaries_extra_args} \
+                ~{"--gcs-project-for-requester-pays " + gcs_project_for_requester_pays}
 
 
             if [[ ! -z "~{normal_bam}" ]]; then
                 gatk --java-options "-Xmx~{command_mem}m" GetPileupSummaries -R ~{ref_fasta} -I ~{normal_bam} ~{"--interval-set-rule INTERSECTION -L " + intervals} \
-                    -V ~{variants_for_contamination} -L ~{variants_for_contamination} -O normal-pileups.table ~{getpileupsummaries_extra_args}
+                    -V ~{variants_for_contamination} -L ~{variants_for_contamination} -O normal-pileups.table ~{getpileupsummaries_extra_args} \
+                    ~{"--gcs-project-for-requester-pays " + gcs_project_for_requester_pays}
             fi
         fi
 
@@ -936,6 +946,7 @@ task FilterAlignmentArtifacts {
       Boolean compress
       File realignment_index_bundle
       String? realignment_extra_args
+      String? gcs_project_for_requester_pays
       Runtime runtime_params
       Int mem
     }
@@ -967,7 +978,8 @@ task FilterAlignmentArtifacts {
             -I ~{bam} \
             --bwa-mem-index-image ~{realignment_index_bundle} \
             ~{realignment_extra_args} \
-            -O ~{output_vcf}
+            -O ~{output_vcf} \
+            ~{"--gcs-project-for-requester-pays " + gcs_project_for_requester_pays}
     }
 
     runtime {
@@ -1014,6 +1026,7 @@ task Funcotate {
        File? interval_list
 
        String? extra_args
+       String? gcs_project_for_requester_pays
 
        # ==============
        Runtime runtime_params
@@ -1095,7 +1108,8 @@ task Funcotate {
              ~{annotation_over_arg}~{default="" sep=" --annotation-override " annotation_overrides} \
              ~{excluded_fields_args}~{default="" sep=" --exclude-field " funcotator_excluded_fields} \
              ~{filter_funcotations_args} \
-             ~{extra_args_arg}
+             ~{extra_args_arg} \
+             ~{"--gcs-project-for-requester-pays " + gcs_project_for_requester_pays}
          # Make sure we have a placeholder index for MAF files so this workflow doesn't fail:
          if [[ "~{output_format}" == "MAF" ]] ; then
             touch ~{output_maf_index}

scripts/mutect2_wdl/mutect2_multi_sample.wdl

@@ -42,6 +42,8 @@ workflow Mutect2_Multi {
     Boolean? compress_vcfs
     Boolean? make_bamout
 
+    String? gcs_project_for_requester_pays
+
     # Oncotator inputs
     String? sequencing_center
     String? sequence_source
@@ -106,7 +108,8 @@ workflow Mutect2_Multi {
                 compress_vcfs = compress_vcfs,
                 gatk_override = gatk_override,
                 gatk_docker = gatk_docker,
-                preemptible = preemptible_attempts
+                preemptible = preemptible_attempts,
+                gcs_project_for_requester_pays = gcs_project_for_requester_pays
         }
     }
 

scripts/mutect2_wdl/mutect2_pon.wdl

@@ -9,7 +9,7 @@ version 1.0
 #  scatter_count: number of parallel jobs when scattering over intervals
 #  pon_name: the resulting panel of normals is {pon_name}.vcf
 #  m2_extra_args: additional command line parameters for Mutect2.  This should not involve --max-mnp-distance,
-#  which the wdl hard-codes to 0 because GenpmicsDBImport can't handle MNPs
+#  which the wdl hard-codes to 0 because GenomicsDBImport can't handle MNPs
 
 import "mutect2.wdl" as m2
 workflow Mutect2_Panel {
@@ -31,6 +31,8 @@ workflow Mutect2_Panel {
     Int? min_contig_size
     Int? create_panel_scatter_count
 
+    String? gcs_project_for_requester_pays
+
     # runtime
     String gatk_docker
     File? gatk_override
@@ -70,7 +72,8 @@ workflow Mutect2_Panel {
                 gatk_override = gatk_override,
                 gatk_docker = gatk_docker,
                 preemptible = preemptible,
-                max_retries = max_retries
+                max_retries = max_retries,
+                gcs_project_for_requester_pays = gcs_project_for_requester_pays
         }
     }