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pipelines/broad/dna_seq/germline/single_sample/exome/example_inputs.json
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| { | ||
| "ExomeGermlineSingleSample.sample_and_unmapped_bams": { | ||
| "sample_name": "NA17-308", | ||
| "base_file_name": "NA17-308", | ||
| "flowcell_unmapped_bams": [ | ||
| "gs://broad-gotc-test-storage/germline_single_sample/exome/scientific/bams/RP-1535.NA17-308/HM5NCBBXX.1.unmapped.bam", | ||
| "gs://broad-gotc-test-storage/germline_single_sample/exome/scientific/bams/RP-1535.NA17-308/HM5NCBBXX.3.unmapped.bam", | ||
| "gs://broad-gotc-test-storage/germline_single_sample/exome/scientific/bams/RP-1535.NA17-308/HM5NCBBXX.4.unmapped.bam", | ||
| "gs://broad-gotc-test-storage/germline_single_sample/exome/scientific/bams/RP-1535.NA17-308/HM5NCBBXX.2.unmapped.bam", | ||
| "gs://broad-gotc-test-storage/germline_single_sample/exome/scientific/bams/RP-1535.NA17-308/HMF2NBBXX.5.unmapped.bam", | ||
| "gs://broad-gotc-test-storage/germline_single_sample/exome/scientific/bams/RP-1535.NA17-308/HMF2NBBXX.6.unmapped.bam", | ||
| "gs://broad-gotc-test-storage/germline_single_sample/exome/scientific/bams/RP-1535.NA17-308/HMF2NBBXX.8.unmapped.bam", | ||
| "gs://broad-gotc-test-storage/germline_single_sample/exome/scientific/bams/RP-1535.NA17-308/HMF2NBBXX.7.unmapped.bam", | ||
| "gs://broad-gotc-test-storage/germline_single_sample/exome/scientific/bams/RP-1535.NA17-308/HMF7MBBXX.3.unmapped.bam", | ||
| "gs://broad-gotc-test-storage/germline_single_sample/exome/scientific/bams/RP-1535.NA17-308/HMF7MBBXX.4.unmapped.bam", | ||
| "gs://broad-gotc-test-storage/germline_single_sample/exome/scientific/bams/RP-1535.NA17-308/HMF7MBBXX.5.unmapped.bam", | ||
| "gs://broad-gotc-test-storage/germline_single_sample/exome/scientific/bams/RP-1535.NA17-308/HMF7MBBXX.1.unmapped.bam", | ||
| "gs://broad-gotc-test-storage/germline_single_sample/exome/scientific/bams/RP-1535.NA17-308/HMF7MBBXX.6.unmapped.bam", | ||
| "gs://broad-gotc-test-storage/germline_single_sample/exome/scientific/bams/RP-1535.NA17-308/HMF7MBBXX.8.unmapped.bam", | ||
| "gs://broad-gotc-test-storage/germline_single_sample/exome/scientific/bams/RP-1535.NA17-308/HMF7MBBXX.7.unmapped.bam", | ||
| "gs://broad-gotc-test-storage/germline_single_sample/exome/scientific/bams/RP-1535.NA17-308/HM5LFBBXX.8.unmapped.bam", | ||
| "gs://broad-gotc-test-storage/germline_single_sample/exome/scientific/bams/RP-1535.NA17-308/HMF7MBBXX.2.unmapped.bam", | ||
| "gs://broad-gotc-test-storage/germline_single_sample/exome/scientific/bams/RP-1535.NA17-308/HM5NCBBXX.5.unmapped.bam" | ||
| ], | ||
| "final_gvcf_base_name": "NA17-308", | ||
| "unmapped_bam_suffix": ".unmapped.bam" | ||
| }, | ||
|
|
||
| "ExomeGermlineSingleSample.references": { | ||
| "contamination_sites_ud": "gs://gcp-public-data--broad-references/hg38/v0/contamination-resources/1000g/1000g.phase3.100k.b38.vcf.gz.dat.UD", | ||
| "contamination_sites_bed": "gs://gcp-public-data--broad-references/hg38/v0/contamination-resources/1000g/1000g.phase3.100k.b38.vcf.gz.dat.bed", | ||
| "contamination_sites_mu": "gs://gcp-public-data--broad-references/hg38/v0/contamination-resources/1000g/1000g.phase3.100k.b38.vcf.gz.dat.mu", | ||
| "calling_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/exome_calling_regions.v1.interval_list", | ||
| "reference_fasta": { | ||
| "ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict", | ||
| "ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta", | ||
| "ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai", | ||
| "ref_alt": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.alt", | ||
| "ref_sa": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.sa", | ||
| "ref_amb": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.amb", | ||
| "ref_bwt": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.bwt", | ||
| "ref_ann": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.ann", | ||
| "ref_pac": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.pac" | ||
| }, | ||
| "known_indels_sites_vcfs": [ | ||
| "gs://gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz", | ||
| "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz" | ||
| ], | ||
| "known_indels_sites_indices": [ | ||
| "gs://gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi", | ||
| "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi" | ||
| ], | ||
| "dbsnp_vcf": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf", | ||
| "dbsnp_vcf_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx", | ||
| "evaluation_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/exome_evaluation_regions.v1.interval_list", | ||
| "haplotype_database_file": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt" | ||
| }, | ||
|
|
||
| "ExomeGermlineSingleSample.scatter_settings": { | ||
| "haplotype_scatter_count": 50, | ||
| "break_bands_at_multiples_of": 0 | ||
| }, | ||
|
|
||
| "ExomeGermlineSingleSample.fingerprint_genotypes_file": "gs://broad-gotc-test-storage/germline_single_sample/exome/scientific/bams/RP-1535.NA17-308/RP-1535.NA17-308.reference.fingerprint.vcf.gz", | ||
| "ExomeGermlineSingleSample.fingerprint_genotypes_index": "gs://broad-gotc-test-storage/germline_single_sample/exome/scientific/bams/RP-1535.NA17-308/RP-1535.NA17-308.reference.fingerprint.vcf.gz.tbi", | ||
| "ExomeGermlineSingleSample.target_interval_list": "gs://broad-references-private/HybSelOligos/whole_exome_illumina_coding_v1/whole_exome_illumina_coding_v1.Homo_sapiens_assembly38.targets.interval_list", | ||
| "ExomeGermlineSingleSample.bait_interval_list": "gs://broad-references-private/HybSelOligos/whole_exome_illumina_coding_v1/whole_exome_illumina_coding_v1.Homo_sapiens_assembly38.baits.interval_list", | ||
| "ExomeGermlineSingleSample.bait_set_name": "whole_exome_illumina_coding_v1", | ||
|
|
||
| "ExomeGermlineSingleSample.papi_settings": { | ||
| "preemptible_tries": 3, | ||
| "agg_preemptible_tries": 3 | ||
| }, | ||
|
|
||
| "ExomeGermlineSingleSample.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false, | ||
| "ExomeGermlineSingleSample.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false | ||
| } |
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pipelines/broad/reprocessing/exome/test_inputs/example_inputs.json
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| { | ||
| "ExomeReprocessing.input_cram": "gs://broad-gotc-test-storage/germline_single_sample/exome/plumbing/truth/{TRUTH_BRANCH}/RP-929.NA12878/NA12878_PLUMBING.cram", | ||
| "ExomeReprocessing.output_map": "gs://broad-gotc-test-storage/germline_single_sample/exome/plumbing/bams/RP-929.NA12878/readgroupid_to_bamfilename_map.txt", | ||
|
|
||
| "ExomeReprocessing.sample_name": "NA12878 PLUMBING", | ||
| "ExomeReprocessing.base_file_name": "RP-929.NA12878", | ||
| "ExomeReprocessing.final_gvcf_base_name": "RP-929.NA12878", | ||
| "ExomeReprocessing.unmapped_bam_suffix": ".unmapped.bam", | ||
|
|
||
| "ExomeReprocessing.references": { | ||
| "contamination_sites_ud": "gs://gcp-public-data--broad-references/hg38/v0/contamination-resources/1000g/1000g.phase3.100k.b38.vcf.gz.dat.UD", | ||
| "contamination_sites_bed": "gs://gcp-public-data--broad-references/hg38/v0/contamination-resources/1000g/1000g.phase3.100k.b38.vcf.gz.dat.bed", | ||
| "contamination_sites_mu": "gs://gcp-public-data--broad-references/hg38/v0/contamination-resources/1000g/1000g.phase3.100k.b38.vcf.gz.dat.mu", | ||
| "calling_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/exome_calling_regions.v1.interval_list", | ||
| "reference_fasta": { | ||
| "ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict", | ||
| "ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta", | ||
| "ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai", | ||
| "ref_alt": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.alt", | ||
| "ref_sa": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.sa", | ||
| "ref_amb": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.amb", | ||
| "ref_bwt": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.bwt", | ||
| "ref_ann": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.ann", | ||
| "ref_pac": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.pac" | ||
| }, | ||
| "known_indels_sites_vcfs": [ | ||
| "gs://gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz", | ||
| "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz" | ||
| ], | ||
| "known_indels_sites_indices": [ | ||
| "gs://gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi", | ||
| "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi" | ||
| ], | ||
| "dbsnp_vcf": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf", | ||
| "dbsnp_vcf_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx", | ||
| "evaluation_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/exome_evaluation_regions.v1.interval_list", | ||
| "haplotype_database_file": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt" | ||
| }, | ||
|
|
||
| "ExomeReprocessing.scatter_settings": { | ||
| "haplotype_scatter_count": 10, | ||
| "break_bands_at_multiples_of": 0 | ||
| }, | ||
|
|
||
| "ExomeReprocessing.fingerprint_genotypes_file": "gs://broad-gotc-test-storage/germline_single_sample/exome/plumbing/bams/RP-929.NA12878/RP-929.NA12878.reference.fingerprint.vcf.gz", | ||
| "ExomeReprocessing.fingerprint_genotypes_index": "gs://broad-gotc-test-storage/germline_single_sample/exome/plumbing/bams/RP-929.NA12878/RP-929.NA12878.reference.fingerprint.vcf.gz.tbi", | ||
|
|
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| "ExomeReprocessing.target_interval_list": "gs://broad-references-private/HybSelOligos/whole_exome_illumina_coding_v1/whole_exome_illumina_coding_v1.Homo_sapiens_assembly38.targets.interval_list", | ||
| "ExomeReprocessing.bait_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/HybSelOligos/whole_exome_illumina_coding_v1/whole_exome_illumina_coding_v1.Homo_sapiens_assembly38.baits.interval_list", | ||
| "ExomeReprocessing.bait_set_name": "whole_exome_illumina_coding_v1", | ||
|
|
||
| "ExomeReprocessing.papi_settings": { | ||
| "preemptible_tries": 3, | ||
| "agg_preemptible_tries": 3 | ||
| }, | ||
|
|
||
| "ExomeReprocessing.ExomeGermlineSingleSample.UnmappedBamToAlignedBam.CheckContamination.disable_sanity_check": true, | ||
| "ExomeReprocessing.ExomeGermlineSingleSample.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false, | ||
| "ExomeReprocessing.ExomeGermlineSingleSample.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false | ||
| } |
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pipelines/broad/reprocessing/external/exome/example_inputs.json
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| { | ||
| "ExternalExomeReprocessing.input_cram": "gs://broad-public-datasets/NA12878/germline_single_sample/exome/plumbing/RP-929.NA12878/NA12878_PLUMBING.cram", | ||
|
|
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| "ExternalExomeReprocessing.sample_name": "NA12878 PLUMBING", | ||
| "ExternalExomeReprocessing.base_file_name": "RP-929.NA12878", | ||
| "ExternalExomeReprocessing.final_gvcf_base_name": "NA12878_PLUMBING", | ||
| "ExternalExomeReprocessing.unmapped_bam_suffix": ".unmapped.bam", | ||
|
|
||
| "ExternalExomeReprocessing.cram_ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta", | ||
| "ExternalExomeReprocessing.cram_ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai", | ||
|
|
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| "ExternalExomeReprocessing.references": { | ||
| "haplotype_database_file": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt", | ||
| "contamination_sites_ud": "gs://gcp-public-data--broad-references/hg38/v0/contamination-resources/1000g/1000g.phase3.100k.b38.vcf.gz.dat.UD", | ||
| "contamination_sites_bed": "gs://gcp-public-data--broad-references/hg38/v0/contamination-resources/1000g/1000g.phase3.100k.b38.vcf.gz.dat.bed", | ||
| "contamination_sites_mu": "gs://gcp-public-data--broad-references/hg38/v0/contamination-resources/1000g/1000g.phase3.100k.b38.vcf.gz.dat.mu", | ||
| "calling_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/exome_calling_regions.v1.interval_list", | ||
| "reference_fasta": { | ||
| "ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict", | ||
| "ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta", | ||
| "ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai", | ||
| "ref_alt": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.alt", | ||
| "ref_sa": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.sa", | ||
| "ref_amb": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.amb", | ||
| "ref_bwt": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.bwt", | ||
| "ref_ann": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.ann", | ||
| "ref_pac": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.pac" | ||
| }, | ||
| "known_indels_sites_vcfs": [ | ||
| "gs://gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz", | ||
| "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz" | ||
| ], | ||
| "known_indels_sites_indices": [ | ||
| "gs://gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi", | ||
| "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi" | ||
| ], | ||
| "dbsnp_vcf": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf", | ||
| "dbsnp_vcf_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx", | ||
| "evaluation_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/exome_evaluation_regions.v1.interval_list" | ||
| }, | ||
|
|
||
| "ExternalExomeReprocessing.scatter_settings": { | ||
| "haplotype_scatter_count": 50, | ||
| "break_bands_at_multiples_of": 0 | ||
| }, | ||
|
|
||
| "ExternalExomeReprocessing.target_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/HybSelOligos/whole_exome_illumina_coding_v1/whole_exome_illumina_coding_v1.Homo_sapiens_assembly38.targets.interval_list", | ||
| "ExternalExomeReprocessing.bait_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/HybSelOligos/whole_exome_illumina_coding_v1/whole_exome_illumina_coding_v1.Homo_sapiens_assembly38.baits.interval_list", | ||
| "ExternalExomeReprocessing.bait_set_name": "whole_exome_illumina_coding_v1", | ||
|
|
||
| "ExternalExomeReprocessing.papi_settings": { | ||
| "preemptible_tries": 3, | ||
| "agg_preemptible_tries": 3 | ||
| }, | ||
|
|
||
| "ExternalExomeReprocessing.ExomeReprocessing.ExomeGermlineSingleSample.UnmappedBamToAlignedBam.CheckContamination.disable_sanity_check": true, | ||
| "ExternalExomeReprocessing.ExomeReprocessing.ExomeGermlineSingleSample.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false, | ||
| "ExternalExomeReprocessing.ExomeReprocessing.ExomeGermlineSingleSample.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false, | ||
|
|
||
| "ExternalExomeReprocessing.destination_cloud_path": "{DESTINATION_CLOUD_PATH}", | ||
| "ExternalExomeReprocessing.vault_token_path": "{VAULT_TOKEN_PATH}", | ||
| "ExternalExomeReprocessing.google_account_vault_path": "{GOOGLE_ACCOUNT_VAULT_PATH}" | ||
| } |