diff --git a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/output_configurations/GatherBatchEvidenceOutputs.json.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/output_configurations/GatherBatchEvidenceOutputs.json.tmpl index d86039a3d..0c3ec1d18 100644 --- a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/output_configurations/GatherBatchEvidenceOutputs.json.tmpl +++ b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/output_configurations/GatherBatchEvidenceOutputs.json.tmpl @@ -30,6 +30,7 @@ "GatherBatchEvidence.std_delly_vcf": "${this.std_delly_vcf}", "GatherBatchEvidence.std_manta_vcf": "${this.std_manta_vcf}", "GatherBatchEvidence.std_melt_vcf": "${this.std_melt_vcf}", + "GatherBatchEvidence.std_scramble_vcf": "${this.std_scramble_vcf}", "GatherBatchEvidence.std_wham_vcf": "${this.std_wham_vcf}", "GatherBatchEvidence.metrics_file_batchevidence": "${this.metrics_file_batchevidence}" } diff --git a/inputs/templates/terra_workspaces/single_sample/GATKSVPipelineSingleSample.no_melt.json.tmpl b/inputs/templates/terra_workspaces/single_sample/GATKSVPipelineSingleSample.no_melt.json.tmpl index ef8db5f61..029812bd7 100644 --- a/inputs/templates/terra_workspaces/single_sample/GATKSVPipelineSingleSample.no_melt.json.tmpl +++ b/inputs/templates/terra_workspaces/single_sample/GATKSVPipelineSingleSample.no_melt.json.tmpl @@ -24,6 +24,7 @@ "GATKSVPipelineSingleSample.bin_exclude": "${workspace.reference_bin_exclude}", + "GATKSVPipelineSingleSample.cloud_sdk_docker": "${workspace.cloud_sdk_docker}", "GATKSVPipelineSingleSample.cnmops_docker": "${workspace.cnmops_docker}", "GATKSVPipelineSingleSample.condense_counts_docker" : "${workspace.condense_counts_docker}", "GATKSVPipelineSingleSample.gatk_docker": "${workspace.gatk_docker}", @@ -106,10 +107,10 @@ "GATKSVPipelineSingleSample.cnmops_mem_gb_override_sample3": 24, - "GATKSVPipelineSingleSample.ref_samples" : {{ ref_panel.samples | tojson }}, - "GATKSVPipelineSingleSample.ref_std_manta_vcfs" : {{ ref_panel.std_manta_vcfs | tojson }}, - "GATKSVPipelineSingleSample.ref_std_wham_vcfs" : {{ ref_panel.std_wham_vcfs | tojson }}, - "GATKSVPipelineSingleSample.ref_pesr_disc_files" : {{ ref_panel.PE_files | tojson }}, - "GATKSVPipelineSingleSample.ref_pesr_split_files" : {{ ref_panel.SR_files | tojson }}, - "GATKSVPipelineSingleSample.gcnv_model_tars" : {{ ref_panel.gcnv_model_tars | tojson }} + "GATKSVPipelineSingleSample.ref_samples_list" : "${workspace.ref_panel_samples_list}", + "GATKSVPipelineSingleSample.ref_std_manta_vcfs_list" : "${workspace.ref_panel_std_manta_vcfs_list}", + "GATKSVPipelineSingleSample.ref_std_wham_vcfs_list" : "${workspace.ref_panel_std_wham_vcfs_list}", + "GATKSVPipelineSingleSample.ref_pesr_disc_files_list" : "${workspace.ref_panel_PE_files_list}", + "GATKSVPipelineSingleSample.ref_pesr_split_files_list" : "${workspace.ref_panel_SR_files_list}", + "GATKSVPipelineSingleSample.gcnv_model_tars_list" : "${workspace.ref_panel_gcnv_model_tars_list}" } diff --git a/inputs/templates/terra_workspaces/single_sample/workspace.tsv.tmpl b/inputs/templates/terra_workspaces/single_sample/workspace.tsv.tmpl index fba39ebfb..7638eb980 100644 --- a/inputs/templates/terra_workspaces/single_sample/workspace.tsv.tmpl +++ b/inputs/templates/terra_workspaces/single_sample/workspace.tsv.tmpl @@ -1,2 +1,2 @@ -workspace:cnmops_docker condense_counts_docker gatk_docker gatk_docker_pesr_override 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 ref_panel_name ref_panel_bincov_matrix ref_panel_contig_ploidy_model_tar ref_panel_cutoffs ref_panel_del_bed ref_panel_dup_bed ref_panel_genotype_pesr_pesr_sepcutoff ref_panel_genotype_pesr_depth_sepcutoff ref_panel_genotype_depth_pesr_sepcutoff ref_panel_genotype_depth_depth_sepcutoff ref_panel_ped_file ref_panel_PE_metrics ref_panel_qc_definitions ref_panel_requester_pays_crams ref_panel_SR_metrics ref_panel_vcf reference_name reference_allosome_file reference_autosome_file reference_bin_exclude reference_cnmops_exclude_list reference_contig_ploidy_priors reference_copy_number_autosomal_contigs reference_cytobands reference_dbsnp_vcf reference_delly_exclude_intervals_file reference_depth_exclude_list reference_empty_file reference_exclude_intervals_for_gcnv_filter_intervals reference_external_af_ref_bed reference_external_af_ref_bed_prefix reference_genome_file reference_inclusion_bed reference_linc_rna_gtf reference_manta_region_bed reference_mei_bed reference_melt_std_vcf_header reference_noncoding_bed reference_pesr_exclude_list reference_preprocessed_intervals reference_primary_contigs_list reference_primary_contigs_fai reference_promoter_bed reference_protein_coding_gtf reference_dict reference_fasta reference_index reference_version reference_rmsk reference_segdups reference_seed_cutoffs reference_unpadded_intervals_file reference_wgd_scoring_mask reference_wham_include_list_bed_file -{{ dockers.cnmops_docker }} {{ dockers.condense_counts_docker }} {{ dockers.gatk_docker }} {{ dockers.gatk_docker_pesr_override }} {{ 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 }} {{ ref_panel.name }} {{ ref_panel.merged_coverage_file }} {{ ref_panel.contig_ploidy_model_tar }} {{ ref_panel.cutoffs }} {{ ref_panel.del_bed }} {{ ref_panel.dup_bed }} {{ ref_panel.genotype_pesr_pesr_sepcutoff }} {{ ref_panel.genotype_pesr_depth_sepcutoff }} {{ ref_panel.genotype_depth_pesr_sepcutoff }} {{ ref_panel.genotype_depth_depth_sepcutoff }} {{ ref_panel.ped_file }} {{ ref_panel.PE_metrics }} {{ reference_resources.single_sample_qc_definitions }} {{ ref_panel.requester_pays_crams }} {{ ref_panel.SR_metrics }} {{ ref_panel.clean_vcf }} {{ reference_resources.name }} {{ reference_resources.allosome_file }} {{ reference_resources.autosome_file }} {{ reference_resources.bin_exclude }} {{ reference_resources.cnmops_exclude_list }} {{ reference_resources.contig_ploidy_priors }} {{ reference_resources.copy_number_autosomal_contigs }} {{ reference_resources.cytobands }} {{ reference_resources.dbsnp_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.inclusion_bed }} {{ reference_resources.linc_rna_gtf }} {{ 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_list }} {{ reference_resources.primary_contigs_fai }} {{ reference_resources.promoter_bed }} {{ reference_resources.protein_coding_gtf }} {{ 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.unpadded_intervals_file }} {{ reference_resources.wgd_scoring_mask }} {{ reference_resources.wham_include_list_bed_file }} +workspace:cloud_sdk_docker cnmops_docker condense_counts_docker gatk_docker gatk_docker_pesr_override 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 ref_panel_name ref_panel_bincov_matrix ref_panel_contig_ploidy_model_tar ref_panel_cutoffs ref_panel_del_bed ref_panel_dup_bed ref_panel_gcnv_model_tars_list ref_panel_genotype_pesr_pesr_sepcutoff ref_panel_genotype_pesr_depth_sepcutoff ref_panel_genotype_depth_pesr_sepcutoff ref_panel_genotype_depth_depth_sepcutoff ref_panel_ped_file ref_panel_PE_files_list ref_panel_PE_metrics ref_panel_qc_definitions ref_panel_requester_pays_crams ref_panel_samples_list ref_panel_SR_files_list ref_panel_SR_metrics ref_panel_std_manta_vcfs_list ref_panel_std_wham_vcfs_list ref_panel_vcf reference_name reference_allosome_file reference_autosome_file reference_bin_exclude reference_cnmops_exclude_list reference_contig_ploidy_priors reference_copy_number_autosomal_contigs reference_cytobands reference_dbsnp_vcf reference_delly_exclude_intervals_file reference_depth_exclude_list reference_empty_file reference_exclude_intervals_for_gcnv_filter_intervals reference_external_af_ref_bed reference_external_af_ref_bed_prefix reference_genome_file reference_inclusion_bed reference_linc_rna_gtf reference_manta_region_bed reference_mei_bed reference_melt_std_vcf_header reference_noncoding_bed reference_pesr_exclude_list reference_preprocessed_intervals reference_primary_contigs_list reference_primary_contigs_fai reference_promoter_bed reference_protein_coding_gtf reference_dict reference_fasta reference_index reference_version reference_rmsk reference_segdups reference_seed_cutoffs reference_unpadded_intervals_file reference_wgd_scoring_mask reference_wham_include_list_bed_file +{{ dockers.cloud_sdk_docker }} {{ dockers.cnmops_docker }} {{ dockers.condense_counts_docker }} {{ dockers.gatk_docker }} {{ dockers.gatk_docker_pesr_override }} {{ 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 }} {{ ref_panel.name }} {{ ref_panel.merged_coverage_file }} {{ ref_panel.contig_ploidy_model_tar }} {{ ref_panel.cutoffs }} {{ ref_panel.del_bed }} {{ ref_panel.dup_bed }} {{ ref_panel.gcnv_model_tars_list }} {{ ref_panel.genotype_pesr_pesr_sepcutoff }} {{ ref_panel.genotype_pesr_depth_sepcutoff }} {{ ref_panel.genotype_depth_pesr_sepcutoff }} {{ ref_panel.genotype_depth_depth_sepcutoff }} {{ ref_panel.ped_file }} {{ ref_panel.PE_files_list }} {{ ref_panel.PE_metrics }} {{ reference_resources.single_sample_qc_definitions }} {{ ref_panel.requester_pays_crams }} {{ ref_panel.samples_list }} {{ ref_panel.SR_files_list }} {{ ref_panel.SR_metrics }} {{ ref_panel.std_manta_vcfs_list }} {{ ref_panel.std_wham_vcfs_list }} {{ ref_panel.clean_vcf }} {{ reference_resources.name }} {{ reference_resources.allosome_file }} {{ reference_resources.autosome_file }} {{ reference_resources.bin_exclude }} {{ reference_resources.cnmops_exclude_list }} {{ reference_resources.contig_ploidy_priors }} {{ reference_resources.copy_number_autosomal_contigs }} {{ reference_resources.cytobands }} {{ reference_resources.dbsnp_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.inclusion_bed }} {{ reference_resources.linc_rna_gtf }} {{ 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_list }} {{ reference_resources.primary_contigs_fai }} {{ reference_resources.promoter_bed }} {{ reference_resources.protein_coding_gtf }} {{ 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.unpadded_intervals_file }} {{ reference_resources.wgd_scoring_mask }} {{ reference_resources.wham_include_list_bed_file }} diff --git a/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.json.tmpl b/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.json.tmpl index f12e2639c..244b51ca8 100644 --- a/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.json.tmpl +++ b/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.json.tmpl @@ -106,11 +106,11 @@ "GATKSVPipelineSingleSample.cnmops_mem_gb_override_sample3": 24, - "GATKSVPipelineSingleSample.ref_samples" : {{ ref_panel.samples | tojson }}, - "GATKSVPipelineSingleSample.ref_std_manta_vcfs" : {{ ref_panel.std_manta_vcfs | tojson }}, - "GATKSVPipelineSingleSample.ref_std_melt_vcfs" : {{ ref_panel.std_melt_vcfs | tojson }}, - "GATKSVPipelineSingleSample.ref_std_wham_vcfs" : {{ ref_panel.std_wham_vcfs | tojson }}, - "GATKSVPipelineSingleSample.ref_pesr_disc_files" : {{ ref_panel.PE_files | tojson }}, - "GATKSVPipelineSingleSample.ref_pesr_split_files" : {{ ref_panel.SR_files | tojson }}, - "GATKSVPipelineSingleSample.gcnv_model_tars" : {{ ref_panel.gcnv_model_tars | tojson }} + "GATKSVPipelineSingleSample.ref_samples_list" : {{ ref_panel.samples_list | tojson }}, + "GATKSVPipelineSingleSample.ref_std_manta_vcfs_list" : {{ ref_panel.std_manta_vcfs_list | tojson }}, + "GATKSVPipelineSingleSample.ref_std_melt_vcfs_list" : {{ ref_panel.std_melt_vcfs_list | tojson }}, + "GATKSVPipelineSingleSample.ref_std_wham_vcfs_list" : {{ ref_panel.std_wham_vcfs_list | tojson }}, + "GATKSVPipelineSingleSample.ref_pesr_disc_files_list" : {{ ref_panel.PE_files_list | tojson }}, + "GATKSVPipelineSingleSample.ref_pesr_split_files_list" : {{ ref_panel.SR_files_list | tojson }}, + "GATKSVPipelineSingleSample.gcnv_model_tars_list" : {{ ref_panel.gcnv_model_tars_list | tojson }} } diff --git a/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.no_melt.json.tmpl b/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.no_melt.json.tmpl index 7e5059419..a6a9c5e1d 100644 --- a/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.no_melt.json.tmpl +++ b/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.no_melt.json.tmpl @@ -107,10 +107,10 @@ "GATKSVPipelineSingleSample.cnmops_mem_gb_override_sample3": 24, - "GATKSVPipelineSingleSample.ref_samples" : {{ ref_panel.samples | tojson }}, - "GATKSVPipelineSingleSample.ref_std_manta_vcfs" : {{ ref_panel.std_manta_vcfs | tojson }}, - "GATKSVPipelineSingleSample.ref_std_wham_vcfs" : {{ ref_panel.std_wham_vcfs | tojson }}, - "GATKSVPipelineSingleSample.ref_pesr_disc_files" : {{ ref_panel.PE_files | tojson }}, - "GATKSVPipelineSingleSample.ref_pesr_split_files" : {{ ref_panel.SR_files | tojson }}, - "GATKSVPipelineSingleSample.gcnv_model_tars" : {{ ref_panel.gcnv_model_tars | tojson }} + "GATKSVPipelineSingleSample.ref_samples_list" : {{ ref_panel.samples_list | tojson }}, + "GATKSVPipelineSingleSample.ref_std_manta_vcfs_list" : {{ ref_panel.std_manta_vcfs_list | tojson }}, + "GATKSVPipelineSingleSample.ref_std_wham_vcfs_list" : {{ ref_panel.std_wham_vcfs_list | tojson }}, + "GATKSVPipelineSingleSample.ref_pesr_disc_files_list" : {{ ref_panel.PE_files_list | tojson }}, + "GATKSVPipelineSingleSample.ref_pesr_split_files_list" : {{ ref_panel.SR_files_list | tojson }}, + "GATKSVPipelineSingleSample.gcnv_model_tars_list" : {{ ref_panel.gcnv_model_tars_list | tojson }} } diff --git a/inputs/values/ref_panel_1kg.json b/inputs/values/ref_panel_1kg.json index 720878baa..8f55e5cde 100644 --- a/inputs/values/ref_panel_1kg.json +++ b/inputs/values/ref_panel_1kg.json @@ -315,6 +315,7 @@ "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GatherSampleEvidenceBatch/GatherSampleEvidenceBatch/bb5e70f1-7186-4e29-96f8-dcb9ee000642/call-GatherSampleEvidence/shard-154/GatherSampleEvidence/f5159902-35ad-4e8e-ac76-2e6278ac387f/call-PESRCollection/PESRCollection/4538b819-c0fe-4d69-bcc1-1658a293e6de/call-RunPESRCollection/cacheCopy/NA21122.disc.txt.gz.tbi", "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GatherSampleEvidenceBatch/GatherSampleEvidenceBatch/bb5e70f1-7186-4e29-96f8-dcb9ee000642/call-GatherSampleEvidence/shard-155/GatherSampleEvidence/9dfac5cf-9a0b-4070-ad5b-2fe087a41856/call-PESRCollection/PESRCollection/066417e3-3848-4dc7-b46e-173fdf2f9ae7/call-RunPESRCollection/cacheCopy/NA21133.disc.txt.gz.tbi" ], + "PE_files_list": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/PE_files_list.txt", "PE_metrics": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GenotypeBatch/GenotypeBatch/ad17f522-0950-4f0a-9148-a13f689082ed/call-GenotypePESRPart1/GenotypePESRPart1/40ec6d76-dd1c-432d-bfab-bc4426d0b1ec/call-TrainPEGenotyping/TrainPEGenotyping/8c1271fd-027d-4669-b516-b41ee77d8997/call-GenotypePEPart1/cacheCopy/ref_panel_1kg.pe_metric_file.txt", "SR_files": [ "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GatherSampleEvidenceBatch/GatherSampleEvidenceBatch/bb5e70f1-7186-4e29-96f8-dcb9ee000642/call-GatherSampleEvidence/shard-0/GatherSampleEvidence/bed8ee84-625c-4d39-99d4-20f9c0462ce6/call-PESRCollection/PESRCollection/57cec0fd-ce5c-4313-b658-6fc26602d820/call-RunPESRCollection/cacheCopy/HG00096.split.txt.gz", @@ -632,6 +633,7 @@ "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GatherSampleEvidenceBatch/GatherSampleEvidenceBatch/bb5e70f1-7186-4e29-96f8-dcb9ee000642/call-GatherSampleEvidence/shard-154/GatherSampleEvidence/f5159902-35ad-4e8e-ac76-2e6278ac387f/call-PESRCollection/PESRCollection/4538b819-c0fe-4d69-bcc1-1658a293e6de/call-RunPESRCollection/cacheCopy/NA21122.split.txt.gz.tbi", "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GatherSampleEvidenceBatch/GatherSampleEvidenceBatch/bb5e70f1-7186-4e29-96f8-dcb9ee000642/call-GatherSampleEvidence/shard-155/GatherSampleEvidence/9dfac5cf-9a0b-4070-ad5b-2fe087a41856/call-PESRCollection/PESRCollection/066417e3-3848-4dc7-b46e-173fdf2f9ae7/call-RunPESRCollection/cacheCopy/NA21133.split.txt.gz.tbi" ], + "SR_files_list": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/SR_files_list.txt", "SR_metrics": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GenotypeBatch/GenotypeBatch/ad17f522-0950-4f0a-9148-a13f689082ed/call-GenotypePESRPart1/GenotypePESRPart1/40ec6d76-dd1c-432d-bfab-bc4426d0b1ec/call-TrainSRGenotyping/TrainSRGenotyping/e81a3092-0c6e-4768-afed-27d7018175dc/call-GenotypeSRPart1/cacheCopy/ref_panel_1kg.sr_metric_file.txt", "bam_or_cram_files": [ "gs://fc-56ac46ea-efc4-4683-b6d5-6d95bed41c5e/CCDG_13607/Project_CCDG_13607_B01_GRM_WGS.cram.2019-02-06/Sample_HG00096/analysis/HG00096.final.cram", @@ -791,8 +793,8 @@ "gs://fc-56ac46ea-efc4-4683-b6d5-6d95bed41c5e/CCDG_13607/Project_CCDG_13607_B01_GRM_WGS.cram.2019-02-06/Sample_NA21122/analysis/NA21122.final.cram", "gs://fc-56ac46ea-efc4-4683-b6d5-6d95bed41c5e/CCDG_13607/Project_CCDG_13607_B01_GRM_WGS.cram.2019-02-06/Sample_NA21133/analysis/NA21133.final.cram" ], - "clean_vcf": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-MakeCohortVcf/MakeCohortVcf/bfd4ef15-d9ea-437b-ade4-bc08e79c29a8/call-CleanVcf/CleanVcf/cda267a8-81b0-46af-aab7-938f8cd42c4f/call-ConcatCleanedVcfs/cacheCopy/ref_panel_1kg.cleaned.vcf.gz", - "clean_vcf_index": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-MakeCohortVcf/MakeCohortVcf/bfd4ef15-d9ea-437b-ade4-bc08e79c29a8/call-CleanVcf/CleanVcf/cda267a8-81b0-46af-aab7-938f8cd42c4f/call-ConcatCleanedVcfs/cacheCopy/ref_panel_1kg.cleaned.vcf.gz.tbi", + "clean_vcf": "gs://gatk-sv-ref-panel-1kg/outputs/MakeCohortVcf/8a209488-c928-449d-92cd-0a5131e92b7c/call-CleanVcf/CleanVcf/277f3f25-bb99-4fe4-a48b-567fd3f344f9/call-ConcatCleanedVcfs/ref_panel_1kg.cleaned.vcf.gz", + "clean_vcf_index": "gs://gatk-sv-ref-panel-1kg/outputs/MakeCohortVcf/8a209488-c928-449d-92cd-0a5131e92b7c/call-CleanVcf/CleanVcf/277f3f25-bb99-4fe4-a48b-567fd3f344f9/call-ConcatCleanedVcfs/ref_panel_1kg.cleaned.vcf.gz.tbi", "cohort_depth_vcf": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GATKSVPipelinePhase1/GATKSVPipelinePhase1/acce2c71-7458-4205-ae13-624f6efc9956/call-FilterBatch/FilterBatch/184defa3-e61c-4757-9962-f685f6d0d204/call-FilterBatchSamples/FilterBatchSamples/b308c32e-d171-4d8d-aeaf-b561c55b06b4/call-ExcludeOutliers/shard-4/cacheCopy/ref_panel_1kg.depth.outliers_removed.vcf.gz", "cohort_pesr_vcf": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GATKSVPipelinePhase1/GATKSVPipelinePhase1/acce2c71-7458-4205-ae13-624f6efc9956/call-FilterBatch/FilterBatch/184defa3-e61c-4757-9962-f685f6d0d204/call-FilterBatchSamples/FilterBatchSamples/b308c32e-d171-4d8d-aeaf-b561c55b06b4/call-MergePesrVcfs/cacheCopy/ref_panel_1kg.filtered_pesr_merged.vcf.gz", "contig_ploidy_model_tar": "gs://gatk-sv-resources-public/hg38/v0/sv-resources/ref-panel/1KG/v2/gcnv/ref_panel_1kg_v2-contig-ploidy-model.tar.gz", @@ -1253,6 +1255,7 @@ "gs://gatk-sv-resources-public/hg38/v0/sv-resources/ref-panel/1KG/v2/gcnv/model_files/ref_panel_1kg_v2-gcnv-model-shard-98.tar.gz", "gs://gatk-sv-resources-public/hg38/v0/sv-resources/ref-panel/1KG/v2/gcnv/model_files/ref_panel_1kg_v2-gcnv-model-shard-99.tar.gz" ], + "gcnv_model_tars_list": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/gcnv_model_tars_list.txt", "genotype_depth_depth_sepcutoff": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GenotypeBatch/GenotypeBatch/ad17f522-0950-4f0a-9148-a13f689082ed/call-GenotypeDepthPart1/GenotypeDepthPart1/be787bb1-25ff-4a54-92a6-2fa6faaee8ec/call-TrainRDGenotyping/TrainRDGenotyping/aa7bc7f2-9779-4242-aa5d-8a8ea4375af9/call-UpdateCutoff/cacheCopy/ref_panel_1kg.depth.depth_sepcutoff.txt", "genotype_depth_pesr_sepcutoff": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GenotypeBatch/GenotypeBatch/ad17f522-0950-4f0a-9148-a13f689082ed/call-GenotypeDepthPart1/GenotypeDepthPart1/be787bb1-25ff-4a54-92a6-2fa6faaee8ec/call-TrainRDGenotyping/TrainRDGenotyping/aa7bc7f2-9779-4242-aa5d-8a8ea4375af9/call-UpdateCutoff/cacheCopy/ref_panel_1kg.depth.pesr_sepcutoff.txt", "genotype_pesr_depth_sepcutoff": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GenotypeBatch/GenotypeBatch/ad17f522-0950-4f0a-9148-a13f689082ed/call-GenotypePESRPart1/GenotypePESRPart1/40ec6d76-dd1c-432d-bfab-bc4426d0b1ec/call-TrainRDGenotyping/TrainRDGenotyping/e5540a96-9072-4719-bcfb-afccdfec15c6/call-UpdateCutoff/cacheCopy/ref_panel_1kg.pesr.depth_sepcutoff.txt", @@ -2236,6 +2239,7 @@ "NA21122", "NA21133" ], + "samples_list": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/samples_list.txt", "sites_filtered_depth_vcf": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GATKSVPipelinePhase1/GATKSVPipelinePhase1/acce2c71-7458-4205-ae13-624f6efc9956/call-FilterBatch/FilterBatch/184defa3-e61c-4757-9962-f685f6d0d204/call-FilterBatchSites/FilterBatchSites/13801c7d-9478-40dc-9a4a-2e80cbab1136/call-FilterAnnotateVcf/shard-4/cacheCopy/ref_panel_1kg.depth.with_evidence.vcf.gz", "sites_filtered_manta_vcf": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GATKSVPipelinePhase1/GATKSVPipelinePhase1/acce2c71-7458-4205-ae13-624f6efc9956/call-FilterBatch/FilterBatch/184defa3-e61c-4757-9962-f685f6d0d204/call-FilterBatchSites/FilterBatchSites/13801c7d-9478-40dc-9a4a-2e80cbab1136/call-FilterAnnotateVcf/shard-0/cacheCopy/ref_panel_1kg.manta.with_evidence.vcf.gz", "sites_filtered_melt_vcf": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GATKSVPipelinePhase1/GATKSVPipelinePhase1/acce2c71-7458-4205-ae13-624f6efc9956/call-FilterBatch/FilterBatch/184defa3-e61c-4757-9962-f685f6d0d204/call-FilterBatchSites/FilterBatchSites/13801c7d-9478-40dc-9a4a-2e80cbab1136/call-FilterAnnotateVcf/shard-3/cacheCopy/ref_panel_1kg.melt.with_evidence.vcf.gz", @@ -2398,6 +2402,7 @@ "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GATKSVPipelinePhase1/GATKSVPipelinePhase1/acce2c71-7458-4205-ae13-624f6efc9956/call-GatherBatchEvidence/GatherBatchEvidence/366e817a-feb2-4d3c-915c-a8bd25529b81/call-PreprocessPESR/PreprocessPESR/69a5b477-c02d-474b-8b5d-eac8e34d49e5/call-StandardizeVCFs/shard-0/cacheCopy/glob-31de091d1940ddb276ce7b6086a74725/std_154.manta.NA21122.vcf.gz", "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GATKSVPipelinePhase1/GATKSVPipelinePhase1/acce2c71-7458-4205-ae13-624f6efc9956/call-GatherBatchEvidence/GatherBatchEvidence/366e817a-feb2-4d3c-915c-a8bd25529b81/call-PreprocessPESR/PreprocessPESR/69a5b477-c02d-474b-8b5d-eac8e34d49e5/call-StandardizeVCFs/shard-0/cacheCopy/glob-31de091d1940ddb276ce7b6086a74725/std_155.manta.NA21133.vcf.gz" ], + "std_manta_vcfs_list": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/std_manta_vcfs_list.txt", "std_melt_vcfs": [ "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GATKSVPipelinePhase1/GATKSVPipelinePhase1/acce2c71-7458-4205-ae13-624f6efc9956/call-GatherBatchEvidence/GatherBatchEvidence/366e817a-feb2-4d3c-915c-a8bd25529b81/call-PreprocessPESR/PreprocessPESR/69a5b477-c02d-474b-8b5d-eac8e34d49e5/call-StandardizeVCFs/shard-2/cacheCopy/glob-31de091d1940ddb276ce7b6086a74725/std_000.melt.HG00096.vcf.gz", "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GATKSVPipelinePhase1/GATKSVPipelinePhase1/acce2c71-7458-4205-ae13-624f6efc9956/call-GatherBatchEvidence/GatherBatchEvidence/366e817a-feb2-4d3c-915c-a8bd25529b81/call-PreprocessPESR/PreprocessPESR/69a5b477-c02d-474b-8b5d-eac8e34d49e5/call-StandardizeVCFs/shard-2/cacheCopy/glob-31de091d1940ddb276ce7b6086a74725/std_001.melt.HG00129.vcf.gz", @@ -2556,6 +2561,7 @@ "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GATKSVPipelinePhase1/GATKSVPipelinePhase1/acce2c71-7458-4205-ae13-624f6efc9956/call-GatherBatchEvidence/GatherBatchEvidence/366e817a-feb2-4d3c-915c-a8bd25529b81/call-PreprocessPESR/PreprocessPESR/69a5b477-c02d-474b-8b5d-eac8e34d49e5/call-StandardizeVCFs/shard-2/cacheCopy/glob-31de091d1940ddb276ce7b6086a74725/std_154.melt.NA21122.vcf.gz", "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GATKSVPipelinePhase1/GATKSVPipelinePhase1/acce2c71-7458-4205-ae13-624f6efc9956/call-GatherBatchEvidence/GatherBatchEvidence/366e817a-feb2-4d3c-915c-a8bd25529b81/call-PreprocessPESR/PreprocessPESR/69a5b477-c02d-474b-8b5d-eac8e34d49e5/call-StandardizeVCFs/shard-2/cacheCopy/glob-31de091d1940ddb276ce7b6086a74725/std_155.melt.NA21133.vcf.gz" ], + "std_melt_vcfs_list": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/std_melt_vcfs_list.txt", "std_wham_vcfs": [ "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GATKSVPipelinePhase1/GATKSVPipelinePhase1/acce2c71-7458-4205-ae13-624f6efc9956/call-GatherBatchEvidence/GatherBatchEvidence/366e817a-feb2-4d3c-915c-a8bd25529b81/call-PreprocessPESR/PreprocessPESR/69a5b477-c02d-474b-8b5d-eac8e34d49e5/call-StandardizeVCFs/shard-3/cacheCopy/glob-31de091d1940ddb276ce7b6086a74725/std_000.wham.HG00096.vcf.gz", "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GATKSVPipelinePhase1/GATKSVPipelinePhase1/acce2c71-7458-4205-ae13-624f6efc9956/call-GatherBatchEvidence/GatherBatchEvidence/366e817a-feb2-4d3c-915c-a8bd25529b81/call-PreprocessPESR/PreprocessPESR/69a5b477-c02d-474b-8b5d-eac8e34d49e5/call-StandardizeVCFs/shard-3/cacheCopy/glob-31de091d1940ddb276ce7b6086a74725/std_001.wham.HG00129.vcf.gz", @@ -2714,6 +2720,7 @@ "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GATKSVPipelinePhase1/GATKSVPipelinePhase1/acce2c71-7458-4205-ae13-624f6efc9956/call-GatherBatchEvidence/GatherBatchEvidence/366e817a-feb2-4d3c-915c-a8bd25529b81/call-PreprocessPESR/PreprocessPESR/69a5b477-c02d-474b-8b5d-eac8e34d49e5/call-StandardizeVCFs/shard-3/cacheCopy/glob-31de091d1940ddb276ce7b6086a74725/std_154.wham.NA21122.vcf.gz", "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GATKSVPipelinePhase1/GATKSVPipelinePhase1/acce2c71-7458-4205-ae13-624f6efc9956/call-GatherBatchEvidence/GatherBatchEvidence/366e817a-feb2-4d3c-915c-a8bd25529b81/call-PreprocessPESR/PreprocessPESR/69a5b477-c02d-474b-8b5d-eac8e34d49e5/call-StandardizeVCFs/shard-3/cacheCopy/glob-31de091d1940ddb276ce7b6086a74725/std_155.wham.NA21133.vcf.gz" ], + "std_wham_vcfs_list": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/std_wham_vcfs_list.txt", "wham_vcfs": [ "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GatherSampleEvidenceBatch/GatherSampleEvidenceBatch/bb5e70f1-7186-4e29-96f8-dcb9ee000642/call-GatherSampleEvidence/shard-0/GatherSampleEvidence/bed8ee84-625c-4d39-99d4-20f9c0462ce6/call-Whamg/Whamg/7309550b-3c8c-45c6-b88e-3ab54e0096cb/call-RunWhamgIncludelist/cacheCopy/HG00096.wham.vcf.gz", "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GatherSampleEvidenceBatch/GatherSampleEvidenceBatch/bb5e70f1-7186-4e29-96f8-dcb9ee000642/call-GatherSampleEvidence/shard-1/GatherSampleEvidence/b623755c-af49-4f7c-98d9-f03d95ab9397/call-Whamg/Whamg/92ef1164-c70d-425c-9733-c3c887789d55/call-RunWhamgIncludelist/cacheCopy/HG00129.wham.vcf.gz", diff --git a/scripts/inputs/create_test_batch.py b/scripts/inputs/create_test_batch.py index e2bae70e5..a64a79cac 100644 --- a/scripts/inputs/create_test_batch.py +++ b/scripts/inputs/create_test_batch.py @@ -7,6 +7,10 @@ import argparse import json import sys +import os +import tempfile +from google.cloud import storage +from urllib.parse import urlparse INPUT_KEYS = set([ @@ -23,6 +27,18 @@ ]) +FILE_LIST_KEYS = set([ + "PE_files", + "SR_files", + "samples", + "std_manta_vcfs", + "std_wham_vcfs", + "std_melt_vcfs", + "std_scramble_vcfs", + "gcnv_model_tars" +]) + + def replace_output_dir_maybe_list(value, execution_bucket, outputs_dir): if outputs_dir is None: return value @@ -38,6 +54,34 @@ def replace_output_dir(value, execution_bucket, outputs_dir): return value.replace(execution_bucket, outputs_dir) +def split_bucket_subdir(directory): + # Parse -b URI input into top-level bucket name (no gs://) and subdirectory path + uri = urlparse(directory) + return uri.netloc, uri.path.lstrip("/") + + +def create_file_list(list_key, values_list, file_list_bucket): + # create tmp file with paths list + list_suffix = ".txt" + fd, fname = tempfile.mkstemp(suffix=list_suffix) + with os.fdopen(fd, 'w') as listfile: + listfile.write("\n".join(values_list)) + + # upload file to GCS + client = storage.Client() + dest_bucket, subdir = split_bucket_subdir(file_list_bucket) + bucket = client.get_bucket(dest_bucket) + gcs_blob_name = os.path.join(subdir, list_key + list_suffix) + blob = bucket.blob(gcs_blob_name) + blob.upload_from_filename(fname) + + # delete tmp file + os.unlink(fname) + + # return the GCS path of the paths list file + return os.path.join("gs://", dest_bucket, gcs_blob_name) + + def main(): parser = argparse.ArgumentParser() parser.add_argument("metadata", help="GATKSVPipelineBatch metadata JSON file") @@ -45,10 +89,12 @@ def main(): "option from Cromwell config file") parser.add_argument("--execution-bucket", help="Cromwell execution bucket, required if " "using --final-workflow-outputs-dir") + parser.add_argument("--file-list-bucket", help="Bucket to which to upload file lists") args = parser.parse_args() execution_bucket = args.execution_bucket outputs_dir = args.final_workflow_outputs_dir + file_list_bucket = args.file_list_bucket if outputs_dir is not None: if execution_bucket is None: raise ValueError("Must supply --execution-bucket if using --final-workflow-outputs-dir") @@ -75,6 +121,11 @@ def main(): f"this entry manually.\n") values[key] = None + if file_list_bucket is not None: + for key in set(values.keys()).intersection(FILE_LIST_KEYS): + list_key = key + "_list" + values[list_key] = create_file_list(list_key, values[key], file_list_bucket) + print(json.dumps(values, sort_keys=True, indent=4)) diff --git a/scripts/test/terra_validation.py b/scripts/test/terra_validation.py index e4324bb8f..7e8403749 100644 --- a/scripts/test/terra_validation.py +++ b/scripts/test/terra_validation.py @@ -31,25 +31,30 @@ """ WDLS_PATH = "wdl/" -TERRA_INPUTS_PATH = "inputs/build/ref_panel_1kg/terra/workflow_configurations/" +TERRA_INPUTS_PATHS = [ + "inputs/build/ref_panel_1kg/terra/workflow_configurations/", + "inputs/build/NA12878/terra/" +] -def list_jsons(inputs_path, expected_num_jsons, subdir="", description=""): - jsons = [os.path.join(subdir, x) for x in listdir(os.path.join(inputs_path, subdir)) if x.endswith(".json")] +def list_jsons(inputs_paths, expected_num_jsons): + jsons = [] + for path in inputs_paths: + jsons.extend([os.path.join(path, x) for x in listdir(path) if x.endswith(".json")]) num_input_jsons = len(jsons) if num_input_jsons < expected_num_jsons: - raise Exception(f"Expected {expected_num_jsons} Terra {description}input JSONs but found {num_input_jsons}.") + raise Exception(f"Expected {expected_num_jsons} Terra input JSONs but found {num_input_jsons}.") jsons.sort() return jsons -def get_wdl_json_pairs(wdl_path, terra_inputs_path, expected_num_inputs): - jsons = list_jsons(terra_inputs_path, expected_num_inputs) +def get_wdl_json_pairs(wdl_path, terra_inputs_paths, expected_num_inputs): + jsons = list_jsons(terra_inputs_paths, expected_num_inputs) for json_file in jsons: path_to_wdl = os.path.join(wdl_path, os.path.basename(json_file).split(".")[0] + ".wdl") if os.path.isfile(path_to_wdl): - yield path_to_wdl, os.path.join(terra_inputs_path, json_file) + yield path_to_wdl, json_file else: logging.warning(f"Can't find WDL corresponding to {os.path.basename(json_file)} at {path_to_wdl}.") @@ -85,7 +90,7 @@ def validate_terra_json(wdl, terra_json, womtool_jar): def validate_all_terra_jsons(base_dir, womtool_jar, expected_num_inputs): successes = 0 for wdl, json_file in get_wdl_json_pairs(os.path.join(base_dir, WDLS_PATH), - os.path.join(base_dir, TERRA_INPUTS_PATH), + [os.path.join(base_dir, x) for x in TERRA_INPUTS_PATHS], expected_num_inputs): successes += validate_terra_json(wdl, json_file, womtool_jar) @@ -103,7 +108,7 @@ def main(): parser.add_argument("-j", "--womtool-jar", help="Path to womtool jar", required=True) parser.add_argument("-n", "--num-input-jsons", help="Number of Terra input JSONs expected", - required=False, default=19, type=int) + required=False, default=20, type=int) parser.add_argument("--log-level", help="Specify level of logging information, ie. info, warning, error (not case-sensitive)", required=False, default="INFO") diff --git a/wdl/GATKSVPipelineSingleSample.wdl b/wdl/GATKSVPipelineSingleSample.wdl index cb80d5cd8..2e74ce741 100644 --- a/wdl/GATKSVPipelineSingleSample.wdl +++ b/wdl/GATKSVPipelineSingleSample.wdl @@ -52,7 +52,7 @@ workflow GATKSVPipelineSingleSample { # Global files File ref_ped_file - Array[String] ref_samples + File ref_samples_list File genome_file File primary_contigs_list File primary_contigs_fai @@ -169,13 +169,13 @@ workflow GATKSVPipelineSingleSample { # gCNV inputs File contig_ploidy_model_tar - Array[File] gcnv_model_tars + File gcnv_model_tars_list # list of files, one per line # bincov counts files (for cn.mops) File ref_panel_bincov_matrix - Array[File] ref_pesr_disc_files - Array[File] ref_pesr_split_files + File ref_pesr_disc_files_list # list of files, one per line + File ref_pesr_split_files_list # list of files, one per line File? gatk4_jar_override Float? gcnv_p_alt @@ -262,10 +262,10 @@ workflow GATKSVPipelineSingleSample { RuntimeAttr? runtime_attr_depth_merge_pre_clusterbatch # Reference panel standardized caller VCFs - Array[File] ref_std_manta_vcfs - Array[File] ref_std_wham_vcfs - Array[File]? ref_std_melt_vcfs - Array[File]? ref_std_scramble_vcfs + File ref_std_manta_vcfs_list # list of files, one per line + File ref_std_wham_vcfs_list # list of files, one per line + File? ref_std_melt_vcfs_list # list of files, one per line + File? ref_std_scramble_vcfs_list # list of files, one per line File ref_panel_del_bed File ref_panel_dup_bed @@ -696,6 +696,8 @@ workflow GATKSVPipelineSingleSample { Array[File] wham_vcfs_ = [select_first([case_wham_vcf, GatherSampleEvidence.wham_vcf])] } + Array[String] ref_samples = read_lines(ref_samples_list) + call batchevidence.GatherBatchEvidence as GatherBatchEvidence { input: batch=batch, @@ -715,12 +717,12 @@ workflow GATKSVPipelineSingleSample { PE_files=[case_pe_file_], cytoband=cytobands, mei_bed=mei_bed, - ref_panel_PE_files=ref_pesr_disc_files, + ref_panel_PE_files=read_lines(ref_pesr_disc_files_list), SR_files=[case_sr_file_], - ref_panel_SR_files=ref_pesr_split_files, + ref_panel_SR_files=read_lines(ref_pesr_split_files_list), inclusion_bed=inclusion_bed, contig_ploidy_model_tar = contig_ploidy_model_tar, - gcnv_model_tars = gcnv_model_tars, + gcnv_model_tars = read_lines(gcnv_model_tars_list), gatk4_jar_override = gatk4_jar_override, run_ploidy = true, append_first_sample_to_ped = true, @@ -807,13 +809,13 @@ workflow GATKSVPipelineSingleSample { File combined_ped_file = select_first([GatherBatchEvidence.combined_ped_file]) # Merge calls with reference panel - Array[File] merged_manta_vcfs_array = flatten([select_first([GatherBatchEvidence.std_manta_vcf]), ref_std_manta_vcfs]) - Array[File] merged_wham_vcfs_array = flatten([select_first([GatherBatchEvidence.std_wham_vcf]), ref_std_wham_vcfs]) + Array[File] merged_manta_vcfs_array = flatten([select_first([GatherBatchEvidence.std_manta_vcf]), read_lines(ref_std_manta_vcfs_list)]) + Array[File] merged_wham_vcfs_array = flatten([select_first([GatherBatchEvidence.std_wham_vcf]), read_lines(ref_std_wham_vcfs_list)]) if (defined(GatherBatchEvidence.std_melt_vcf)) { - Array[File]? merged_melt_vcfs_array = flatten([select_first([GatherBatchEvidence.std_melt_vcf]), select_first([ref_std_melt_vcfs])]) + Array[File]? merged_melt_vcfs_array = flatten([select_first([GatherBatchEvidence.std_melt_vcf]), read_lines(select_first([ref_std_melt_vcfs_list]))]) } if (defined(GatherBatchEvidence.std_scramble_vcf)) { - Array[File]? merged_scramble_vcfs_array = flatten([select_first([GatherBatchEvidence.std_scramble_vcf]), select_first([ref_std_scramble_vcfs])]) + Array[File]? merged_scramble_vcfs_array = flatten([select_first([GatherBatchEvidence.std_scramble_vcf]), read_lines(select_first([ref_std_scramble_vcfs_list]))]) } call dpn.MergeSet as MergeSetDel {