From bbf273fad634c6940804e5ad6a406c1a4fff9ba9 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Sat, 16 Oct 2021 15:38:33 +0200 Subject: [PATCH] Create examples using public gs link from the broad-references-private sources --- .../single_sample/exome/example_inputs.json | 77 +++++++++++++++++++ .../exome/test_inputs/example_inputs.json | 60 +++++++++++++++ .../external/exome/example_inputs.json | 63 +++++++++++++++ 3 files changed, 200 insertions(+) create mode 100644 pipelines/broad/dna_seq/germline/single_sample/exome/example_inputs.json create mode 100644 pipelines/broad/reprocessing/exome/test_inputs/example_inputs.json create mode 100644 pipelines/broad/reprocessing/external/exome/example_inputs.json diff --git a/pipelines/broad/dna_seq/germline/single_sample/exome/example_inputs.json b/pipelines/broad/dna_seq/germline/single_sample/exome/example_inputs.json new file mode 100644 index 000000000..ab6c47221 --- /dev/null +++ b/pipelines/broad/dna_seq/germline/single_sample/exome/example_inputs.json @@ -0,0 +1,77 @@ +{ + "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 +} diff --git a/pipelines/broad/reprocessing/exome/test_inputs/example_inputs.json b/pipelines/broad/reprocessing/exome/test_inputs/example_inputs.json new file mode 100644 index 000000000..08de85eb7 --- /dev/null +++ b/pipelines/broad/reprocessing/exome/test_inputs/example_inputs.json @@ -0,0 +1,60 @@ +{ + "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", + + "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 +} diff --git a/pipelines/broad/reprocessing/external/exome/example_inputs.json b/pipelines/broad/reprocessing/external/exome/example_inputs.json new file mode 100644 index 000000000..740f2ac31 --- /dev/null +++ b/pipelines/broad/reprocessing/external/exome/example_inputs.json @@ -0,0 +1,63 @@ +{ + "ExternalExomeReprocessing.input_cram": "gs://broad-public-datasets/NA12878/germline_single_sample/exome/plumbing/RP-929.NA12878/NA12878_PLUMBING.cram", + + "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", + + "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}" +}