Improve on Scramble integration (#386)

* Improve on Scramble integration.

* Revert adding scramble to module 10.

* Add scramble_vcfs to EvidenceQC.json.tmpl.

* Add Scramble docker to Terra workspace template.

* Add scramble to Terra templates.

* revert EvidenceQC.json.tmpl change

* revert an r-script change.

* Remove scramble_vcf from test template but add to Terra template.

inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/ClusterBatch.json.tmpl

@@ -27,5 +27,6 @@
   "ClusterBatch.wham_vcf_tar": "${this.std_wham_vcf_tar}",
   "ClusterBatch.manta_vcf_tar": "${this.std_manta_vcf_tar}",
   "ClusterBatch.melt_vcf_tar": "${this.std_melt_vcf_tar}",
+  "ClusterBatch.scramble_vcf_tar": "${this.std_scramble_vcf_tar}",
   "ClusterBatch.ped_file": "${this.cohort_ped_file}"
 }

inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/EvidenceQC.json.tmpl

@@ -12,5 +12,6 @@
   "EvidenceQC.manta_vcfs": "${this.samples.manta_vcf}",
   "EvidenceQC.melt_vcfs": "${this.samples.melt_vcf}",
   "EvidenceQC.wham_vcfs": "${this.samples.wham_vcf}",
+  "EvidenceQC.scramble_vcfs": "${this.samples.scramble_vcf}",
   "EvidenceQC.samples": "${this.samples.sample_id}"
 }

inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/FilterBatchSamples.json.tmpl

@@ -10,5 +10,6 @@
   "FilterBatchSamples.delly_vcf" : "${this.sites_filtered_delly_vcf}",
   "FilterBatchSamples.wham_vcf" : "${this.sites_filtered_wham_vcf}",
   "FilterBatchSamples.melt_vcf" : "${this.sites_filtered_melt_vcf}",
+  "FilterBatchSamples.scramble_vcf" : "${this.sites_filtered_scramble_vcf}",
   "FilterBatchSamples.depth_vcf" : "${this.sites_filtered_depth_vcf}"
 }

inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/FilterBatchSites.json.tmpl

@@ -6,6 +6,7 @@
   "FilterBatchSites.manta_vcf" : "${this.clustered_manta_vcf}",
   "FilterBatchSites.wham_vcf" : "${this.clustered_wham_vcf}",
   "FilterBatchSites.melt_vcf" : "${this.clustered_melt_vcf}",
+  "FilterBatchSites.scramble_vcf" : "${this.clustered_scramble_vcf}",
   "FilterBatchSites.evidence_metrics": "${this.metrics}",
   "FilterBatchSites.evidence_metrics_common": "${this.metrics_common}"
 }

inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/GatherBatchEvidence.json.tmpl

@@ -57,5 +57,6 @@
   "GatherBatchEvidence.manta_vcfs": "${this.samples.manta_vcf}",
   "GatherBatchEvidence.samples": "${this.samples.sample_id}",
   "GatherBatchEvidence.melt_vcfs": "${this.samples.melt_vcf}",
-  "GatherBatchEvidence.wham_vcfs": "${this.samples.wham_vcf}"
+  "GatherBatchEvidence.wham_vcfs": "${this.samples.wham_vcf}",
+  "GatherBatchEvidence.scramble_vcfs": "${this.samples.scramble_vcf}"
 }

inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/GenerateBatchMetrics.json.tmpl

@@ -30,5 +30,6 @@
   "GenerateBatchMetrics.depth_vcf" : "${this.clustered_depth_vcf}",
   "GenerateBatchMetrics.manta_vcf" : "${this.clustered_manta_vcf}",
   "GenerateBatchMetrics.wham_vcf" : "${this.clustered_wham_vcf}",
+  "GenerateBatchMetrics.scramble_vcf" : "${this.clustered_scramble_vcf}",
   "GenerateBatchMetrics.melt_vcf" : "${this.clustered_melt_vcf}"
 }

inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/PlotSVCountsPerSample.json.tmpl

@@ -4,5 +4,5 @@
   "PlotSVCountsPerSample.N_IQR_cutoff": "6",
 
   "PlotSVCountsPerSample.prefix": "${this.sample_set_id}",
-  "PlotSVCountsPerSample.vcfs" : "${[this.sites_filtered_manta_vcf, this.sites_filtered_delly_vcf, this.sites_filtered_wham_vcf, this.sites_filtered_melt_vcf, this.sites_filtered_depth_vcf]}"
+  "PlotSVCountsPerSample.vcfs" : "${[this.sites_filtered_manta_vcf, this.sites_filtered_delly_vcf, this.sites_filtered_wham_vcf, this.sites_filtered_melt_vcf, this.sites_filtered_scramble_vcf, this.sites_filtered_depth_vcf]}"
 }

inputs/templates/terra_workspaces/cohort_mode/workspace.tsv.tmpl

@@ -1,2 +1,2 @@
-workspace:cloud_sdk_docker	cnmops_docker	condense_counts_docker	gatk_docker	gatk_docker_pesr_override	gcnv_gatk_docker	genomes_in_the_cloud_docker	linux_docker	manta_docker	samtools_cloud_docker	sv_base_docker	sv_base_mini_docker	sv_pipeline_base_docker	sv_pipeline_docker	sv_pipeline_hail_docker	sv_pipeline_updates_docker	sv_pipeline_qc_docker	sv_pipeline_rdtest_docker	wham_docker	allosome_file	autosome_file	bin_exclude	cnmops_exclude_list	cohort_ped_file	contig_ploidy_priors	copy_number_autosomal_contigs	cytobands	sd_locs_vcf	delly_exclude_intervals_file	depth_exclude_list	empty_file	exclude_intervals_for_gcnv_filter_intervals	external_af_ref_bed	external_af_ref_bed_prefix	genome_file	manta_region_bed	mei_bed	melt_standard_vcf_header	noncoding_bed	pesr_exclude_list	preprocessed_intervals	primary_contigs_fai	primary_contigs_list	protein_coding_gtf	reference_build	reference_dict	reference_fasta	reference_index	reference_version	rmsk	segdups	seed_cutoffs	wgd_scoring_mask	wham_include_list_bed_file	chr_x	chr_y
-{{ dockers.cloud_sdk_docker }}	{{ dockers.cnmops_docker }}	{{ dockers.condense_counts_docker }}	{{ dockers.gatk_docker }}	{{ dockers.gatk_docker_pesr_override }}	{{ dockers.gatk_docker }}	{{ dockers.genomes_in_the_cloud_docker }}	{{ dockers.linux_docker }}	{{ dockers.manta_docker }}	{{ dockers.samtools_cloud_docker }}	{{ dockers.sv_base_docker }}	{{ dockers.sv_base_mini_docker }}	{{ dockers.sv_pipeline_base_docker }}	{{ dockers.sv_pipeline_docker }}	{{ dockers.sv_pipeline_hail_docker }}	{{ dockers.sv_pipeline_updates_docker }}	{{ dockers.sv_pipeline_qc_docker }}	{{ dockers.sv_pipeline_rdtest_docker }}	{{ dockers.wham_docker }}	{{ reference_resources.allosome_file }}	{{ reference_resources.autosome_file }}	{{ reference_resources.bin_exclude }}	{{ reference_resources.cnmops_exclude_list }}	gs://broad-dsde-methods-eph/ped_1kgp_all.ped	{{ reference_resources.contig_ploidy_priors }}	{{ reference_resources.copy_number_autosomal_contigs }}	{{ reference_resources.cytobands }}	{{ reference_resources.sd_locs_vcf }}	{{ reference_resources.delly_exclude_intervals_file }}	{{ reference_resources.depth_exclude_list }}	{{ reference_resources.empty_file }}	{{ reference_resources.exclude_intervals_for_gcnv_filter_intervals }}	{{ reference_resources.external_af_ref_bed }}	{{ reference_resources.external_af_ref_bed_prefix }}	{{ reference_resources.genome_file }}	{{ reference_resources.manta_region_bed }}	{{ reference_resources.mei_bed }}	{{ reference_resources.melt_std_vcf_header }}	{{ reference_resources.noncoding_bed }}	{{ reference_resources.pesr_exclude_list }}	{{ reference_resources.preprocessed_intervals }}	{{ reference_resources.primary_contigs_fai }}	{{ reference_resources.primary_contigs_list }}	{{ reference_resources.protein_coding_gtf }}	{{ reference_resources.reference_build }}	{{ reference_resources.reference_dict }}	{{ reference_resources.reference_fasta }}	{{ reference_resources.reference_index }}	{{ reference_resources.reference_version }}	{{ reference_resources.rmsk }}	{{ reference_resources.segdups }}	{{ reference_resources.seed_cutoffs }}	{{ reference_resources.wgd_scoring_mask }}	{{ reference_resources.wham_include_list_bed_file }}	{{ reference_resources.chr_x }}	{{ reference_resources.chr_y }}
+workspace:cloud_sdk_docker	cnmops_docker	condense_counts_docker	gatk_docker	gatk_docker_pesr_override	gcnv_gatk_docker	genomes_in_the_cloud_docker	linux_docker	manta_docker	samtools_cloud_docker	sv_base_docker	sv_base_mini_docker	sv_pipeline_base_docker	sv_pipeline_docker	sv_pipeline_hail_docker	sv_pipeline_updates_docker	sv_pipeline_qc_docker	sv_pipeline_rdtest_docker	wham_docker	scramble_docker	allosome_file	autosome_file	bin_exclude	cnmops_exclude_list	cohort_ped_file	contig_ploidy_priors	copy_number_autosomal_contigs	cytobands	sd_locs_vcf	delly_exclude_intervals_file	depth_exclude_list	empty_file	exclude_intervals_for_gcnv_filter_intervals	external_af_ref_bed	external_af_ref_bed_prefix	genome_file	manta_region_bed	mei_bed	melt_standard_vcf_header	noncoding_bed	pesr_exclude_list	preprocessed_intervals	primary_contigs_fai	primary_contigs_list	protein_coding_gtf	reference_build	reference_dict	reference_fasta	reference_index	reference_version	rmsk	segdups	seed_cutoffs	wgd_scoring_mask	wham_include_list_bed_file	chr_x	chr_y
+{{ dockers.cloud_sdk_docker }}	{{ dockers.cnmops_docker }}	{{ dockers.condense_counts_docker }}	{{ dockers.gatk_docker }}	{{ dockers.gatk_docker_pesr_override }}	{{ dockers.gatk_docker }}	{{ dockers.genomes_in_the_cloud_docker }}	{{ dockers.linux_docker }}	{{ dockers.manta_docker }}	{{ dockers.samtools_cloud_docker }}	{{ dockers.sv_base_docker }}	{{ dockers.sv_base_mini_docker }}	{{ dockers.sv_pipeline_base_docker }}	{{ dockers.sv_pipeline_docker }}	{{ dockers.sv_pipeline_hail_docker }}	{{ dockers.sv_pipeline_updates_docker }}	{{ dockers.sv_pipeline_qc_docker }}	{{ dockers.sv_pipeline_rdtest_docker }}	{{ dockers.wham_docker }}	{{ dockers.scramble_docker }}	{{ reference_resources.allosome_file }}	{{ reference_resources.autosome_file }}	{{ reference_resources.bin_exclude }}	{{ reference_resources.cnmops_exclude_list }}	gs://broad-dsde-methods-eph/ped_1kgp_all.ped	{{ reference_resources.contig_ploidy_priors }}	{{ reference_resources.copy_number_autosomal_contigs }}	{{ reference_resources.cytobands }}	{{ reference_resources.sd_locs_vcf }}	{{ reference_resources.delly_exclude_intervals_file }}	{{ reference_resources.depth_exclude_list }}	{{ reference_resources.empty_file }}	{{ reference_resources.exclude_intervals_for_gcnv_filter_intervals }}	{{ reference_resources.external_af_ref_bed }}	{{ reference_resources.external_af_ref_bed_prefix }}	{{ reference_resources.genome_file }}	{{ reference_resources.manta_region_bed }}	{{ reference_resources.mei_bed }}	{{ reference_resources.melt_std_vcf_header }}	{{ reference_resources.noncoding_bed }}	{{ reference_resources.pesr_exclude_list }}	{{ reference_resources.preprocessed_intervals }}	{{ reference_resources.primary_contigs_fai }}	{{ reference_resources.primary_contigs_list }}	{{ reference_resources.protein_coding_gtf }}	{{ reference_resources.reference_build }}	{{ reference_resources.reference_dict }}	{{ reference_resources.reference_fasta }}	{{ reference_resources.reference_index }}	{{ reference_resources.reference_version }}	{{ reference_resources.rmsk }}	{{ reference_resources.segdups }}	{{ reference_resources.seed_cutoffs }}	{{ reference_resources.wgd_scoring_mask }}	{{ reference_resources.wham_include_list_bed_file }}	{{ reference_resources.chr_x }}	{{ reference_resources.chr_y }}

wdl/EvidenceQC.wdl

@@ -32,6 +32,7 @@ workflow EvidenceQC {
     Array[File]? delly_vcfs        # Delly VCF
     Array[File]? melt_vcfs         # Melt VCF
     Array[File]? wham_vcfs         # Wham VCF
+    Array[File]? scramble_vcfs     # Scramble VCF
 
     # WGD files
     File wgd_scoring_mask
@@ -147,6 +148,17 @@ workflow EvidenceQC {
           runtime_attr_outlier = runtime_attr_qc_outlier
       }
     }
+    if (defined(scramble_vcfs) && (length(select_first([scramble_vcfs])) > 0)) {
+      call vcfqc.RawVcfQC as RawVcfQC_Scramble {
+        input:
+          vcfs = select_first([scramble_vcfs]),
+          prefix = batch,
+          caller = "Scramble",
+          runtime_attr_qc = runtime_attr_qc,
+          sv_pipeline_docker = sv_pipeline_docker,
+          runtime_attr_outlier = runtime_attr_qc_outlier
+      }
+    }
   }
 
   output {
@@ -158,6 +170,8 @@ workflow EvidenceQC {
     File? melt_qc_high = RawVcfQC_Melt.high
     File? wham_qc_low = RawVcfQC_Wham.low
     File? wham_qc_high = RawVcfQC_Wham.high
+    File? scramble_qc_low = RawVcfQC_Scramble.low
+    File? scramble_qc_high = RawVcfQC_Scramble.high
 
     File? ploidy_matrix = Ploidy.ploidy_matrix
     File? ploidy_plots = Ploidy.ploidy_plots