diff --git a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/EvidenceQC.json.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/EvidenceQC.json.tmpl index 273ccba36..4823fa32e 100644 --- a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/EvidenceQC.json.tmpl +++ b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/EvidenceQC.json.tmpl @@ -5,11 +5,10 @@ "EvidenceQC.sv_pipeline_qc_docker": "${workspace.sv_pipeline_qc_docker}", "EvidenceQC.sv_base_docker": "${workspace.sv_base_docker}", "EvidenceQC.wgd_scoring_mask": "${workspace.wgd_scoring_mask}", - "EvidenceQC.genome_file": "${workspace.genome_file}", "EvidenceQC.batch": "${this.sample_set_id}", "EvidenceQC.melt_insert_size": "${this.samples.melt_insert_size}", - "EvidenceQC.counts": "${this.samples.coverage_counts}", + "EvidenceQC.coverage_counts": "${this.samples.coverage_counts}", "EvidenceQC.manta_vcfs": "${this.samples.manta_vcf}", "EvidenceQC.melt_vcfs": "${this.samples.melt_vcf}", "EvidenceQC.wham_vcfs": "${this.samples.wham_vcf}", diff --git a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/GatherBatchEvidence.json.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/GatherBatchEvidence.json.tmpl index 473938355..c2cab6236 100644 --- a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/GatherBatchEvidence.json.tmpl +++ b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/GatherBatchEvidence.json.tmpl @@ -53,7 +53,7 @@ "GatherBatchEvidence.PE_files": "${this.samples.pesr_disc}", "GatherBatchEvidence.SR_files": "${this.samples.pesr_split}", "GatherBatchEvidence.SD_files": "${this.samples.pesr_sd}", - "GatherBatchEvidence.counts": "${this.samples.coverage_counts}", + "GatherBatchEvidence.coverage_counts": "${this.samples.coverage_counts}", "GatherBatchEvidence.manta_vcfs": "${this.samples.manta_vcf}", "GatherBatchEvidence.samples": "${this.samples.sample_id}", "GatherBatchEvidence.melt_vcfs": "${this.samples.melt_vcf}", diff --git a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/TrainGCNV.json.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/TrainGCNV.json.tmpl index d99462381..7ab459df8 100644 --- a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/TrainGCNV.json.tmpl +++ b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/TrainGCNV.json.tmpl @@ -58,7 +58,7 @@ "TrainGCNV.ploidy_sample_psi_scale" : 0.001, "TrainGCNV.cohort": "${this.sample_set_id}", - "TrainGCNV.count_files": "${this.samples.coverage_counts}", + "TrainGCNV.coverage_counts": "${this.samples.coverage_counts}", "TrainGCNV.samples": "${this.samples.sample_id}", "TrainGCNV.n_samples_subsample": 100, diff --git a/inputs/templates/test/EvidenceQC/EvidenceQC.json.tmpl b/inputs/templates/test/EvidenceQC/EvidenceQC.json.tmpl index b3937d578..fa04ca077 100644 --- a/inputs/templates/test/EvidenceQC/EvidenceQC.json.tmpl +++ b/inputs/templates/test/EvidenceQC/EvidenceQC.json.tmpl @@ -5,10 +5,9 @@ "EvidenceQC.sv_pipeline_qc_docker": {{ dockers.sv_pipeline_qc_docker | tojson }}, "EvidenceQC.sv_base_docker": {{ dockers.sv_base_docker | tojson }}, "EvidenceQC.wgd_scoring_mask": {{ reference_resources.wgd_scoring_mask | tojson }}, - "EvidenceQC.genome_file": {{ reference_resources.genome_file | tojson }}, "EvidenceQC.batch": {{ test_batch.name | tojson }}, - "EvidenceQC.counts": {{ test_batch.counts | tojson }}, + "EvidenceQC.coverage_counts": {{ test_batch.counts | tojson }}, "EvidenceQC.manta_vcfs": {{ test_batch.manta_vcfs | tojson }}, "EvidenceQC.melt_vcfs": {{ test_batch.melt_vcfs | tojson }}, "EvidenceQC.wham_vcfs": {{ test_batch.wham_vcfs | tojson }}, diff --git a/inputs/templates/test/GatherBatchEvidence/GatherBatchEvidence.json.tmpl b/inputs/templates/test/GatherBatchEvidence/GatherBatchEvidence.json.tmpl index 01f9b9fe3..213dded7c 100644 --- a/inputs/templates/test/GatherBatchEvidence/GatherBatchEvidence.json.tmpl +++ b/inputs/templates/test/GatherBatchEvidence/GatherBatchEvidence.json.tmpl @@ -52,7 +52,7 @@ "GatherBatchEvidence.PE_files": {{ test_batch.PE_files | tojson }}, "GatherBatchEvidence.SR_files": {{ test_batch.SR_files | tojson }}, "GatherBatchEvidence.SD_files": {{ test_batch.SD_files | tojson }}, - "GatherBatchEvidence.counts": {{ test_batch.counts | tojson }}, + "GatherBatchEvidence.coverage_counts": {{ test_batch.counts | tojson }}, "GatherBatchEvidence.manta_vcfs": {{ test_batch.manta_vcfs | tojson }}, "GatherBatchEvidence.samples": {{ test_batch.samples | tojson }}, "GatherBatchEvidence.melt_vcfs": {{ test_batch.melt_vcfs | tojson }}, diff --git a/inputs/templates/test/TrainGCNV/TrainGCNV.json.tmpl b/inputs/templates/test/TrainGCNV/TrainGCNV.json.tmpl index 3c1f10359..b5b990896 100644 --- a/inputs/templates/test/TrainGCNV/TrainGCNV.json.tmpl +++ b/inputs/templates/test/TrainGCNV/TrainGCNV.json.tmpl @@ -58,6 +58,6 @@ "TrainGCNV.ploidy_sample_psi_scale" : 0.001, "TrainGCNV.cohort": {{ test_batch.name | tojson }}, - "TrainGCNV.count_files": {{ test_batch.counts | tojson }}, + "TrainGCNV.coverage_counts": {{ test_batch.counts | tojson }}, "TrainGCNV.samples": {{ test_batch.samples | tojson }} } diff --git a/wdl/CollectCoverage.wdl b/wdl/CollectCoverage.wdl index 0de5c9f8b..eefa7b8ba 100644 --- a/wdl/CollectCoverage.wdl +++ b/wdl/CollectCoverage.wdl @@ -78,7 +78,7 @@ task CollectCounts { task CondenseReadCounts { input { - File counts + File coverage_counts String sample Int? max_interval_size Int? min_interval_size @@ -103,8 +103,8 @@ task CondenseReadCounts { set -euo pipefail export GATK_LOCAL_JAR=~{default="/root/gatk.jar" gatk4_jar_override} - zcat ~{counts} | grep '^@' | grep -v '@RG' > ref.dict - zcat ~{counts} | grep -v '^@' | sed -e 1d | \ + zcat ~{coverage_counts} | grep '^@' | grep -v '@RG' > ref.dict + zcat ~{coverage_counts} | grep -v '^@' | sed -e 1d | \ awk 'BEGIN{FS=OFS="\t";print "#Chr\tStart\tEnd\tNA21133"}{print $1,$2-1,$3,$4}' | bgzip > in.rd.txt.gz tabix -0 -s1 -b2 -e3 in.rd.txt.gz gatk --java-options -Xmx2g CondenseDepthEvidence -F in.rd.txt.gz -O out.rd.txt.gz --sequence-dictionary ref.dict \ diff --git a/wdl/EvidenceQC.wdl b/wdl/EvidenceQC.wdl index 91daa1ab4..659a684bb 100644 --- a/wdl/EvidenceQC.wdl +++ b/wdl/EvidenceQC.wdl @@ -21,11 +21,8 @@ workflow EvidenceQC { # Optional QC tasks Boolean run_vcf_qc - # Global files - File genome_file - # Coverage files - Array[File] counts + Array[File] coverage_counts # SV tool calls Array[File]? manta_vcfs # Manta VCF @@ -65,7 +62,7 @@ workflow EvidenceQC { call mbm.MakeBincovMatrix as MakeBincovMatrix { input: samples = samples, - count_files = counts, + coverage_counts = coverage_counts, batch = batch, disk_overhead_gb = disk_overhead_bincov_gb, sv_base_mini_docker = sv_base_mini_docker, diff --git a/wdl/GatherBatchEvidence.wdl b/wdl/GatherBatchEvidence.wdl index f3f01a7e1..04a5189b8 100644 --- a/wdl/GatherBatchEvidence.wdl +++ b/wdl/GatherBatchEvidence.wdl @@ -40,7 +40,7 @@ workflow GatherBatchEvidence { # PE/SR/BAF/bincov files # If neither SD_files nor ref_panel_SD_files is present, BAF_files must be supplied # If BAF_files is absent, SD_files and/or ref_panel_SD_files and sd_locs_vcf must be supplied - Array[File] counts + Array[File] coverage_counts File? ref_panel_bincov_matrix File? bincov_matrix File? bincov_matrix_index @@ -189,7 +189,7 @@ workflow GatherBatchEvidence { call mbm.MakeBincovMatrix as MakeBincovMatrix { input: samples = samples, - count_files = counts, + coverage_counts = coverage_counts, bincov_matrix = ref_panel_bincov_matrix, bincov_matrix_samples = ref_panel_samples, batch = batch, @@ -311,7 +311,7 @@ workflow GatherBatchEvidence { scatter (i in range(length(samples))) { call cov.CondenseReadCounts as CondenseReadCounts { input: - counts = counts[i], + coverage_counts = coverage_counts[i], sample = samples[i], min_interval_size = min_interval_size, max_interval_size = max_interval_size, diff --git a/wdl/MakeBincovMatrix.wdl b/wdl/MakeBincovMatrix.wdl index d17aa0427..ca569d94c 100644 --- a/wdl/MakeBincovMatrix.wdl +++ b/wdl/MakeBincovMatrix.wdl @@ -5,7 +5,7 @@ import "Structs.wdl" workflow MakeBincovMatrix { input { Array[String] samples - Array[File] count_files + Array[File] coverage_counts Array[String]? bincov_matrix_samples File? bincov_matrix String batch @@ -30,7 +30,7 @@ workflow MakeBincovMatrix { } Array[String]+ all_samples = flatten([samples, select_all([bincov_matrix_header])]) - Array[File]+ all_count_files = flatten([count_files, select_all([bincov_matrix])]) + Array[File]+ all_count_files = flatten([coverage_counts, select_all([bincov_matrix])]) scatter(i in range(length(all_count_files))) { call MakeBincovMatrixColumns { diff --git a/wdl/TrainGCNV.wdl b/wdl/TrainGCNV.wdl index 579d1255e..82c40de3a 100644 --- a/wdl/TrainGCNV.wdl +++ b/wdl/TrainGCNV.wdl @@ -9,7 +9,7 @@ import "Utils.wdl" as util workflow TrainGCNV { input { Array[String] samples - Array[File] count_files + Array[File] coverage_counts # Common parameters String cohort @@ -129,7 +129,7 @@ workflow TrainGCNV { String sample_ids_ = samples[i] call cov.CondenseReadCounts as CondenseReadCounts { input: - counts = count_files[i], + counts = coverage_counts[i], sample = samples[i], min_interval_size = min_interval_size, max_interval_size = max_interval_size,