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…estsForGdaArray Three new GDA samples for Arrays testing.
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34 changes: 34 additions & 0 deletions
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pipelines/broad/arrays/single_sample/test_inputs/Scientific/204520870050_R02C01_NA24385.json
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| { | ||
| "Arrays.chip_well_barcode": "204520870050_R02C01", | ||
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| "Arrays.sample_alias": "243320540", | ||
| "Arrays.sample_id": "SM-K5P2W", | ||
| "Arrays.sample_lsid": "org.broadinstitute:crsp:K5P2W", | ||
| "Arrays.reported_gender": "Male", | ||
| "Arrays.product_type": "aou_array", | ||
| "Arrays.regulatory_designation": "CLINICAL_DIAGNOSTICS", | ||
| "Arrays.research_project_id": "RP-1710", | ||
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| "Arrays.call_rate_threshold": 0.98, | ||
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| "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GDA-8v1-0_A5/idats/204520870050_R02C01/204520870050_R02C01_Grn.idat", | ||
| "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GDA-8v1-0_A5/idats/204520870050_R02C01/204520870050_R02C01_Red.idat", | ||
|
|
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| "Arrays.bead_pool_manifest_file": "gs://broad-gotc-test-storage/arrays/metadata/GDA-8v1-0_A5/GDA-8v1-0_A5.bpm", | ||
| "Arrays.extended_chip_manifest_file": "gs://broad-gotc-test-storage/arrays/metadata/GDA-8v1-0_A5/GDA-8v1-0_A5.1.5.extended.csv", | ||
| "Arrays.cluster_file": "gs://broad-gotc-test-storage/arrays/metadata/GDA-8v1-0_A5/GDA-8v1-0_A1_ClusterFile.egt", | ||
|
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| "Arrays.ref_fasta": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta", | ||
| "Arrays.ref_fasta_index": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.fai", | ||
| "Arrays.ref_dict": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.dict", | ||
| "Arrays.dbSNP_vcf": "gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz", | ||
| "Arrays.dbSNP_vcf_index": "gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz.tbi", | ||
| "Arrays.haplotype_database_file": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.haplotype_database.txt", | ||
| "Arrays.variant_rsids_file": "gs://broad-references-private/hg19/v0/Homo_sapiens_assembly19.haplotype_database.snps.list", | ||
| "Arrays.minor_allele_frequency_file": "gs://broad-gotc-test-storage/arrays/metadata/GDA-8v1-0_A5/GDA-8v1-0_A5.MAF.txt", | ||
|
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| "Arrays.disk_size": 100, | ||
| "Arrays.preemptible_tries": 3, | ||
| "Arrays.vault_token_path": "{VAULT_TOKEN_PATH}", | ||
| "Arrays.environment": "{ENV}" | ||
| } |
34 changes: 34 additions & 0 deletions
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pipelines/broad/arrays/single_sample/test_inputs/Scientific/204520870050_R04C01_NA24143.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| { | ||
| "Arrays.chip_well_barcode": "204520870050_R04C01", | ||
|
|
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| "Arrays.sample_alias": "243320539", | ||
| "Arrays.sample_id": "SM-K5P3L", | ||
| "Arrays.sample_lsid": "org.broadinstitute:crsp:K5P3L", | ||
| "Arrays.reported_gender": "Female", | ||
| "Arrays.product_type": "aou_array", | ||
| "Arrays.regulatory_designation": "CLINICAL_DIAGNOSTICS", | ||
| "Arrays.research_project_id": "RP-1710", | ||
|
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| "Arrays.call_rate_threshold": 0.98, | ||
|
|
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| "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GDA-8v1-0_A5/idats/204520870050_R04C01/204520870050_R04C01_Grn.idat", | ||
| "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GDA-8v1-0_A5/idats/204520870050_R04C01/204520870050_R04C01_Red.idat", | ||
|
|
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| "Arrays.bead_pool_manifest_file": "gs://broad-gotc-test-storage/arrays/metadata/GDA-8v1-0_A5/GDA-8v1-0_A5.bpm", | ||
| "Arrays.extended_chip_manifest_file": "gs://broad-gotc-test-storage/arrays/metadata/GDA-8v1-0_A5/GDA-8v1-0_A5.1.5.extended.csv", | ||
| "Arrays.cluster_file": "gs://broad-gotc-test-storage/arrays/metadata/GDA-8v1-0_A5/GDA-8v1-0_A1_ClusterFile.egt", | ||
|
|
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| "Arrays.ref_fasta": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta", | ||
| "Arrays.ref_fasta_index": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.fai", | ||
| "Arrays.ref_dict": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.dict", | ||
| "Arrays.dbSNP_vcf": "gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz", | ||
| "Arrays.dbSNP_vcf_index": "gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz.tbi", | ||
| "Arrays.haplotype_database_file": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.haplotype_database.txt", | ||
| "Arrays.variant_rsids_file": "gs://broad-references-private/hg19/v0/Homo_sapiens_assembly19.haplotype_database.snps.list", | ||
| "Arrays.minor_allele_frequency_file": "gs://broad-gotc-test-storage/arrays/metadata/GDA-8v1-0_A5/GDA-8v1-0_A5.MAF.txt", | ||
|
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| "Arrays.disk_size": 100, | ||
| "Arrays.preemptible_tries": 3, | ||
| "Arrays.vault_token_path": "{VAULT_TOKEN_PATH}", | ||
| "Arrays.environment": "{ENV}" | ||
| } |
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pipelines/broad/arrays/single_sample/test_inputs/Scientific/204520870050_R06C01_NA24149.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| { | ||
| "Arrays.chip_well_barcode": "204520870050_R06C01", | ||
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| "Arrays.sample_alias": "243320543", | ||
| "Arrays.sample_id": "SM-K5P4A", | ||
| "Arrays.sample_lsid": "org.broadinstitute:crsp:K5P4A", | ||
| "Arrays.reported_gender": "Male", | ||
| "Arrays.product_type": "aou_array", | ||
| "Arrays.regulatory_designation": "CLINICAL_DIAGNOSTICS", | ||
| "Arrays.research_project_id": "RP-1710", | ||
|
|
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| "Arrays.call_rate_threshold": 0.98, | ||
|
|
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| "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GDA-8v1-0_A5/idats/204520870050_R06C01/204520870050_R06C01_Grn.idat", | ||
| "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GDA-8v1-0_A5/idats/204520870050_R06C01/204520870050_R06C01_Red.idat", | ||
|
|
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| "Arrays.bead_pool_manifest_file": "gs://broad-gotc-test-storage/arrays/metadata/GDA-8v1-0_A5/GDA-8v1-0_A5.bpm", | ||
| "Arrays.extended_chip_manifest_file": "gs://broad-gotc-test-storage/arrays/metadata/GDA-8v1-0_A5/GDA-8v1-0_A5.1.5.extended.csv", | ||
| "Arrays.cluster_file": "gs://broad-gotc-test-storage/arrays/metadata/GDA-8v1-0_A5/GDA-8v1-0_A1_ClusterFile.egt", | ||
|
|
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| "Arrays.ref_fasta": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta", | ||
| "Arrays.ref_fasta_index": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.fai", | ||
| "Arrays.ref_dict": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.dict", | ||
| "Arrays.dbSNP_vcf": "gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz", | ||
| "Arrays.dbSNP_vcf_index": "gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz.tbi", | ||
| "Arrays.haplotype_database_file": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.haplotype_database.txt", | ||
| "Arrays.variant_rsids_file": "gs://broad-references-private/hg19/v0/Homo_sapiens_assembly19.haplotype_database.snps.list", | ||
| "Arrays.minor_allele_frequency_file": "gs://broad-gotc-test-storage/arrays/metadata/GDA-8v1-0_A5/GDA-8v1-0_A5.MAF.txt", | ||
|
|
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| "Arrays.disk_size": 100, | ||
| "Arrays.preemptible_tries": 3, | ||
| "Arrays.vault_token_path": "{VAULT_TOKEN_PATH}", | ||
| "Arrays.environment": "{ENV}" | ||
| } |
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26 changes: 26 additions & 0 deletions
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pipelines/broad/genotyping/illumina/test_inputs/Scientific/204520870050_R02C01_NA24385.json
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| { | ||
| "IlluminaGenotypingArray.sample_alias": "NA24385", | ||
| "IlluminaGenotypingArray.analysis_version_number": 1, | ||
| "IlluminaGenotypingArray.call_rate_threshold": 0.98, | ||
| "IlluminaGenotypingArray.reported_gender": "Male", | ||
| "IlluminaGenotypingArray.chip_well_barcode": "204520870050_R02C01", | ||
|
|
||
| "IlluminaGenotypingArray.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GDA-8v1-0_A5/idats/204520870050_R02C01/204520870050_R02C01_Grn.idat", | ||
| "IlluminaGenotypingArray.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GDA-8v1-0_A5/idats/204520870050_R02C01/204520870050_R02C01_Red.idat", | ||
|
|
||
| "IlluminaGenotypingArray.bead_pool_manifest_file": "gs://broad-gotc-test-storage/arrays/metadata/GDA-8v1-0_A5/GDA-8v1-0_A5.bpm", | ||
| "IlluminaGenotypingArray.extended_chip_manifest_file": "gs://broad-gotc-test-storage/arrays/metadata/GDA-8v1-0_A5/GDA-8v1-0_A5.1.5.extended.csv", | ||
| "IlluminaGenotypingArray.cluster_file": "gs://broad-gotc-test-storage/arrays/metadata/GDA-8v1-0_A5/GDA-8v1-0_A1_ClusterFile.egt", | ||
|
|
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| "IlluminaGenotypingArray.disk_size": 100, | ||
|
|
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| "IlluminaGenotypingArray.ref_fasta": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta", | ||
| "IlluminaGenotypingArray.ref_fasta_index": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.fai", | ||
| "IlluminaGenotypingArray.ref_dict": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.dict", | ||
| "IlluminaGenotypingArray.dbSNP_vcf": "gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz", | ||
| "IlluminaGenotypingArray.dbSNP_vcf_index": "gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz.tbi", | ||
| "IlluminaGenotypingArray.haplotype_database_file": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.haplotype_database.txt", | ||
| "IlluminaGenotypingArray.variant_rsids_file": "gs://broad-references-private/hg19/v0/Homo_sapiens_assembly19.haplotype_database.snps.list", | ||
| "IlluminaGenotypingArray.minor_allele_frequency_file": "gs://broad-gotc-test-storage/arrays/metadata/GDA-8v1-0_A5/GDA-8v1-0_A5.MAF.txt", | ||
| "IlluminaGenotypingArray.preemptible_tries": 3 | ||
| } |
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pipelines/broad/genotyping/illumina/test_inputs/Scientific/204520870050_R04C01_NA24143.json
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| Original file line number | Diff line number | Diff line change |
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| { | ||
| "IlluminaGenotypingArray.sample_alias": "NA24143", | ||
| "IlluminaGenotypingArray.analysis_version_number": 1, | ||
| "IlluminaGenotypingArray.call_rate_threshold": 0.98, | ||
| "IlluminaGenotypingArray.reported_gender": "Female", | ||
| "IlluminaGenotypingArray.chip_well_barcode": "204520870050_R04C01", | ||
|
|
||
| "IlluminaGenotypingArray.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GDA-8v1-0_A5/idats/204520870050_R04C01/204520870050_R04C01_Grn.idat", | ||
| "IlluminaGenotypingArray.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GDA-8v1-0_A5/idats/204520870050_R04C01/204520870050_R04C01_Red.idat", | ||
|
|
||
| "IlluminaGenotypingArray.bead_pool_manifest_file": "gs://broad-gotc-test-storage/arrays/metadata/GDA-8v1-0_A5/GDA-8v1-0_A5.bpm", | ||
| "IlluminaGenotypingArray.extended_chip_manifest_file": "gs://broad-gotc-test-storage/arrays/metadata/GDA-8v1-0_A5/GDA-8v1-0_A5.1.5.extended.csv", | ||
| "IlluminaGenotypingArray.cluster_file": "gs://broad-gotc-test-storage/arrays/metadata/GDA-8v1-0_A5/GDA-8v1-0_A1_ClusterFile.egt", | ||
|
|
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| "IlluminaGenotypingArray.disk_size": 100, | ||
|
|
||
| "IlluminaGenotypingArray.ref_fasta": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta", | ||
| "IlluminaGenotypingArray.ref_fasta_index": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.fai", | ||
| "IlluminaGenotypingArray.ref_dict": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.dict", | ||
| "IlluminaGenotypingArray.dbSNP_vcf": "gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz", | ||
| "IlluminaGenotypingArray.dbSNP_vcf_index": "gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz.tbi", | ||
| "IlluminaGenotypingArray.haplotype_database_file": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.haplotype_database.txt", | ||
| "IlluminaGenotypingArray.variant_rsids_file": "gs://broad-references-private/hg19/v0/Homo_sapiens_assembly19.haplotype_database.snps.list", | ||
| "IlluminaGenotypingArray.minor_allele_frequency_file": "gs://broad-gotc-test-storage/arrays/metadata/GDA-8v1-0_A5/GDA-8v1-0_A5.MAF.txt", | ||
| "IlluminaGenotypingArray.preemptible_tries": 3 | ||
| } |
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pipelines/broad/genotyping/illumina/test_inputs/Scientific/204520870050_R06C01_NA24149.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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| { | ||
| "IlluminaGenotypingArray.sample_alias": "NA24149", | ||
| "IlluminaGenotypingArray.analysis_version_number": 1, | ||
| "IlluminaGenotypingArray.call_rate_threshold": 0.98, | ||
| "IlluminaGenotypingArray.reported_gender": "Male", | ||
| "IlluminaGenotypingArray.chip_well_barcode": "204520870050_R06C01", | ||
|
|
||
| "IlluminaGenotypingArray.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GDA-8v1-0_A5/idats/204520870050_R06C01/204520870050_R06C01_Grn.idat", | ||
| "IlluminaGenotypingArray.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GDA-8v1-0_A5/idats/204520870050_R06C01/204520870050_R06C01_Red.idat", | ||
|
|
||
| "IlluminaGenotypingArray.bead_pool_manifest_file": "gs://broad-gotc-test-storage/arrays/metadata/GDA-8v1-0_A5/GDA-8v1-0_A5.bpm", | ||
| "IlluminaGenotypingArray.extended_chip_manifest_file": "gs://broad-gotc-test-storage/arrays/metadata/GDA-8v1-0_A5/GDA-8v1-0_A5.1.5.extended.csv", | ||
| "IlluminaGenotypingArray.cluster_file": "gs://broad-gotc-test-storage/arrays/metadata/GDA-8v1-0_A5/GDA-8v1-0_A1_ClusterFile.egt", | ||
|
|
||
| "IlluminaGenotypingArray.disk_size": 100, | ||
|
|
||
| "IlluminaGenotypingArray.ref_fasta": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta", | ||
| "IlluminaGenotypingArray.ref_fasta_index": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.fai", | ||
| "IlluminaGenotypingArray.ref_dict": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.dict", | ||
| "IlluminaGenotypingArray.dbSNP_vcf": "gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz", | ||
| "IlluminaGenotypingArray.dbSNP_vcf_index": "gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz.tbi", | ||
| "IlluminaGenotypingArray.haplotype_database_file": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.haplotype_database.txt", | ||
| "IlluminaGenotypingArray.variant_rsids_file": "gs://broad-references-private/hg19/v0/Homo_sapiens_assembly19.haplotype_database.snps.list", | ||
| "IlluminaGenotypingArray.minor_allele_frequency_file": "gs://broad-gotc-test-storage/arrays/metadata/GDA-8v1-0_A5/GDA-8v1-0_A5.MAF.txt", | ||
| "IlluminaGenotypingArray.preemptible_tries": 3 | ||
| } |