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Follow up to 2nd round of gnomAD MakeCohortVcf updates (#290)
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* remove inputs for deleted task from single sample WDL. follow up to #288

* change spaces to tabs in terra workspace.tsv templates

* add back sanitize_filter_field.py call
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@epiercehoffman
epiercehoffman authored Feb 3, 2022
1 parent dd9f115 commit ab8a855
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4 changes: 2 additions & 2 deletions input_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
{{ 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 }}
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
{{ 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 }}
4 changes: 2 additions & 2 deletions input_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.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_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: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.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_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: 1 addition & 0 deletions wdl/CleanVcfChromosome.wdl
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Expand Up @@ -727,6 +727,7 @@ task FinalCleanup {
--prefix ~{prefix} \
~{vcf} stdout \
| fgrep -v "##INFO=<ID=HIGH_SR_BACKGROUND" \
| /opt/sv-pipeline/04_variant_resolution/scripts/sanitize_filter_field.py stdin stdout \
| fgrep -v "##INFO=<ID=MEMBERS,Number=.,Type=String," \
| bgzip -c \
> ~{prefix}.vcf.gz
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6 changes: 0 additions & 6 deletions wdl/GATKSVPipelineSingleSample.wdl
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Expand Up @@ -396,7 +396,6 @@ workflow GATKSVPipelineSingleSample {
RuntimeAttr? runtime_override_breakpoint_overlap_filter
# overrides for mini tasks
RuntimeAttr? runtime_override_ids_from_vcf
RuntimeAttr? runtime_override_clean_background_fail
RuntimeAttr? runtime_override_make_cpx_cnv_input_file
RuntimeAttr? runtime_override_subset_inversions
Expand Down Expand Up @@ -474,8 +473,6 @@ workflow GATKSVPipelineSingleSample {
RuntimeAttr? runtime_override_fix_header_regeno
# overrides for CleanVcfContig
RuntimeAttr? runtime_attr_ids_from_vcf_clean
RuntimeAttr? runtime_attr_subset_ped_clean
RuntimeAttr? runtime_override_preconcat_clean_final
RuntimeAttr? runtime_override_hail_merge_clean_final
RuntimeAttr? runtime_override_fix_header_clean_final
Expand Down Expand Up @@ -1109,7 +1106,6 @@ workflow GATKSVPipelineSingleSample {
runtime_override_rename_variants=runtime_override_rename_variants,
runtime_override_rename_cleaned_samples=runtime_override_rename_cleaned_samples,
runtime_override_breakpoint_overlap_filter=runtime_override_breakpoint_overlap_filter,
runtime_override_ids_from_vcf=runtime_override_ids_from_vcf,
runtime_override_clean_background_fail=runtime_override_clean_background_fail,
runtime_override_make_cpx_cnv_input_file=runtime_override_make_cpx_cnv_input_file,
runtime_override_subset_inversions=runtime_override_subset_inversions,
Expand Down Expand Up @@ -1177,8 +1173,6 @@ workflow GATKSVPipelineSingleSample {
runtime_override_preconcat_regeno=runtime_override_preconcat_regeno,
runtime_override_hail_merge_regeno=runtime_override_hail_merge_regeno,
runtime_override_fix_header_regeno=runtime_override_fix_header_regeno,
runtime_attr_ids_from_vcf_clean=runtime_attr_ids_from_vcf_clean,
runtime_attr_subset_ped_clean=runtime_attr_subset_ped_clean,
runtime_override_preconcat_clean_final=runtime_override_preconcat_clean_final,
runtime_override_hail_merge_clean_final=runtime_override_hail_merge_clean_final,
runtime_override_fix_header_clean_final=runtime_override_fix_header_clean_final,
Expand Down

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