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Update GATK versions #324

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Update GATK versions #324

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8689d80
Update gatk
mwalker174 Mar 19, 2022
41fafd2
Update dockers
mwalker174 Mar 29, 2022
093e843
Fix pesr collection tabix
mwalker174 Mar 29, 2022
5197373
Bump up PostprocessGermlineCNVCalls memory
mwalker174 Mar 30, 2022
6fa42ef
Turn off scramble in tests
mwalker174 Mar 30, 2022
4de6418
Don't try to tabix evidence files produced by PrintSVEvidence
mwalker174 Mar 30, 2022
0a8bdd7
Remove --skip-header option from PrintSVEvidence
mwalker174 Mar 31, 2022
9de6c9e
Update GATK in sv-base-virtual-env
mwalker174 May 2, 2022
de6e117
Update gatk docker to 4.2.6.1
mwalker174 May 5, 2022
7d10b4b
Update sv-base-virtual-env docker with lastest gatk commit (again); u…
mwalker174 May 10, 2022
46d48e7
Update dockers
mwalker174 May 11, 2022
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2 changes: 1 addition & 1 deletion dockerfiles/sv-base-virtual-env/Dockerfile
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ARG UBUNTU_RELEASE="18.04"
ARG R_RELEASE_VERSION="3.6.3"
ARG GATK_COMMIT="a33bf19dd3188af0af1bd17bce015eb20ba73227"
ARG GATK_COMMIT="a3141f79b2971e023f009f64231f3643d312a18e"
ARG GATK_JAR="/opt/gatk.jar"
ARG VIRTUAL_ENV_PATH="/gatk-sv-env"

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1 change: 0 additions & 1 deletion ...lates/terra_workspaces/cohort_mode/workflow_configurations/GatherSampleEvidence.json.tmpl
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"GatherSampleEvidence.wham_docker": "${workspace.wham_docker}",
"GatherSampleEvidence.genomes_in_the_cloud_docker" : "${workspace.genomes_in_the_cloud_docker}",
"GatherSampleEvidence.gatk_docker" : "${workspace.gatk_docker}",
"GatherSampleEvidence.gatk_docker_pesr_override": "${workspace.gatk_docker_pesr_override}",
"GatherSampleEvidence.cloud_sdk_docker": "${workspace.cloud_sdk_docker}",

"GatherSampleEvidence.primary_contigs_fai": "${workspace.primary_contigs_fai}",
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4 changes: 2 additions & 2 deletions inputs/templates/terra_workspaces/cohort_mode/workspace.tsv.tmpl
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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 dbsnp_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 inclusion_bed linc_rna_gtf manta_region_bed mei_bed melt_standard_vcf_header noncoding_bed pesr_exclude_list preprocessed_intervals primary_contigs_fai primary_contigs_list promoter_bed protein_coding_gtf reference_build reference_dict reference_fasta reference_index reference_version rmsk segdups seed_cutoffs unpadded_intervals_file wgd_scoring_mask wham_include_list_bed_file chr_x chr_y google_project_id
{{ 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.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 | tojson }} {{ reference_resources.external_af_ref_bed_prefix | tojson }} {{ reference_resources.genome_file }} {{ reference_resources.inclusion_bed }} {{ reference_resources.linc_rna_gtf | tojson }} {{ reference_resources.manta_region_bed }} {{ reference_resources.mei_bed }} {{ reference_resources.melt_std_vcf_header }} {{ reference_resources.noncoding_bed | tojson }} {{ reference_resources.pesr_exclude_list }} {{ reference_resources.preprocessed_intervals }} {{ reference_resources.primary_contigs_fai }} {{ reference_resources.primary_contigs_list }} {{ reference_resources.promoter_bed | tojson }} {{ reference_resources.protein_coding_gtf | tojson }} {{ 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.unpadded_intervals_file }} {{ reference_resources.wgd_scoring_mask }} {{ reference_resources.wham_include_list_bed_file }} {{ reference_resources.chr_x }} {{ reference_resources.chr_y }} {{ cloud_env.terra_billing_project_id }}
workspace:cloud_sdk_docker cnmops_docker condense_counts_docker 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 dbsnp_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 inclusion_bed linc_rna_gtf manta_region_bed mei_bed melt_standard_vcf_header noncoding_bed pesr_exclude_list preprocessed_intervals primary_contigs_fai primary_contigs_list promoter_bed protein_coding_gtf reference_build reference_dict reference_fasta reference_index reference_version rmsk segdups seed_cutoffs unpadded_intervals_file wgd_scoring_mask wham_include_list_bed_file chr_x chr_y google_project_id
{{ dockers.cloud_sdk_docker }} {{ dockers.cnmops_docker }} {{ dockers.condense_counts_docker }} {{ dockers.gatk_docker }} {{ 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.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 | tojson }} {{ reference_resources.external_af_ref_bed_prefix | tojson }} {{ reference_resources.genome_file }} {{ reference_resources.inclusion_bed }} {{ reference_resources.linc_rna_gtf | tojson }} {{ reference_resources.manta_region_bed }} {{ reference_resources.mei_bed }} {{ reference_resources.melt_std_vcf_header }} {{ reference_resources.noncoding_bed | tojson }} {{ reference_resources.pesr_exclude_list }} {{ reference_resources.preprocessed_intervals }} {{ reference_resources.primary_contigs_fai }} {{ reference_resources.primary_contigs_list }} {{ reference_resources.promoter_bed | tojson }} {{ reference_resources.protein_coding_gtf | tojson }} {{ 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.unpadded_intervals_file }} {{ reference_resources.wgd_scoring_mask }} {{ reference_resources.wham_include_list_bed_file }} {{ reference_resources.chr_x }} {{ reference_resources.chr_y }} {{ cloud_env.terra_billing_project_id }}
1 change: 0 additions & 1 deletion inputs/templates/terra_workspaces/single_sample/GATKSVPipelineSingleSample.no_melt.json.tmpl
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"GATKSVPipelineSingleSample.cnmops_docker": "${workspace.cnmops_docker}",
"GATKSVPipelineSingleSample.condense_counts_docker" : "${workspace.condense_counts_docker}",
"GATKSVPipelineSingleSample.gatk_docker": "${workspace.gatk_docker}",
"GATKSVPipelineSingleSample.gatk_docker_pesr_override" : "${workspace.gatk_docker}",
"GATKSVPipelineSingleSample.genomes_in_the_cloud_docker" : "${workspace.genomes_in_the_cloud_docker}",

"GATKSVPipelineSingleSample.linux_docker" : "${workspace.linux_docker}",
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4 changes: 2 additions & 2 deletions inputs/templates/terra_workspaces/single_sample/workspace.tsv.tmpl
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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 }}
workspace:cloud_sdk_docker cnmops_docker condense_counts_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 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.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 }}
1 change: 0 additions & 1 deletion inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.FromSampleEvidence.json.tmpl
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"GATKSVPipelineBatch.cnmops_docker": {{ dockers.cnmops_docker | tojson }},
"GATKSVPipelineBatch.linux_docker" : {{ dockers.linux_docker | tojson }},
"GATKSVPipelineBatch.gatk_docker": {{ dockers.gatk_docker | tojson }},
"GATKSVPipelineBatch.gatk_docker_pesr_override" : {{ dockers.gatk_docker | tojson }},
"GATKSVPipelineBatch.condense_counts_docker" : {{ dockers.condense_counts_docker | tojson }},
"GATKSVPipelineBatch.genomes_in_the_cloud_docker" : {{ dockers.genomes_in_the_cloud_docker | tojson }},
"GATKSVPipelineBatch.sv_base_docker": {{ dockers.sv_base_docker | tojson }},
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5 changes: 2 additions & 3 deletions inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.json.tmpl
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"GATKSVPipelineBatch.use_delly": "false",
"GATKSVPipelineBatch.use_manta": "true",
"GATKSVPipelineBatch.use_wham": "true",
"GATKSVPipelineBatch.use_melt": "false",
"GATKSVPipelineBatch.use_scramble": "true",
"GATKSVPipelineBatch.use_melt": "true",
"GATKSVPipelineBatch.use_scramble": "false",

"GATKSVPipelineBatch.GATKSVPipelinePhase1.gvcf_gcs_project_for_requester_pays" : {{ cloud_env.google_project_id | tojson }},

Expand All @@ -23,7 +23,6 @@
"GATKSVPipelineBatch.cnmops_docker": {{ dockers.cnmops_docker | tojson }},
"GATKSVPipelineBatch.linux_docker" : {{ dockers.linux_docker | tojson }},
"GATKSVPipelineBatch.gatk_docker": {{ dockers.gatk_docker | tojson }},
"GATKSVPipelineBatch.gatk_docker_pesr_override" : {{ dockers.gatk_docker | tojson }},
"GATKSVPipelineBatch.condense_counts_docker" : {{ dockers.condense_counts_docker | tojson }},
"GATKSVPipelineBatch.genomes_in_the_cloud_docker" : {{ dockers.genomes_in_the_cloud_docker | tojson }},
"GATKSVPipelineBatch.scramble_docker" : {{ dockers.scramble_docker | tojson }},
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