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Replace Array[File] with File inputs in single-sample pipeline (#338)
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* replace ref panel file arrays with list files for single-sample pipeline
* single samp terra workspace config fixes
* update ref panel clean VCF after fixing ends and rescaling GQ
* validate single sample json during terra validation script
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@epiercehoffman
epiercehoffman authored Apr 29, 2022
1 parent 9ddf0c6 commit e6c21c5
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Showing 9 changed files with 114 additions and 47 deletions.
1 change: 1 addition & 0 deletions ...t_mode/workflow_configurations/output_configurations/GatherBatchEvidenceOutputs.json.tmpl
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Expand Up @@ -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}"
}
13 changes: 7 additions & 6 deletions inputs/templates/terra_workspaces/single_sample/GATKSVPipelineSingleSample.no_melt.json.tmpl
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Expand Up @@ -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}",
Expand Down Expand Up @@ -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}"
}
4 changes: 2 additions & 2 deletions inputs/templates/terra_workspaces/single_sample/workspace.tsv.tmpl
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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 }}
14 changes: 7 additions & 7 deletions inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.json.tmpl
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Expand Up @@ -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 }}
}
12 changes: 6 additions & 6 deletions ...ts/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.no_melt.json.tmpl
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Expand Up @@ -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 }}
}
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