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PairedEndSingleSampleWf.hg38.inputs.json
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PairedEndSingleSampleWf.hg38.inputs.json
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{
"##_COMMENT1": "Take note of the .64 extensions on the reference files, issues between 32 and 64 bit OS",
"##_COMMENT2": "SAMPLE NAME AND UNMAPPED BAMS - read the README to find other examples.",
"PairedEndSingleSampleWorkflow.sample_name": "NA12878",
"PairedEndSingleSampleWorkflow.base_file_name": "NA12878",
"PairedEndSingleSampleWorkflow.flowcell_unmapped_bams": ["gs://broad-public-datasets/NA12878_downsampled_for_testing/unmapped/H06HDADXX130110.1.ATCACGAT.20k_reads.bam",
"gs://broad-public-datasets/NA12878_downsampled_for_testing/unmapped/H06HDADXX130110.2.ATCACGAT.20k_reads.bam",
"gs://broad-public-datasets/NA12878_downsampled_for_testing/unmapped/H06JUADXX130110.1.ATCACGAT.20k_reads.bam"],
"PairedEndSingleSampleWorkflow.final_gvcf_base_name": "NA12878",
"PairedEndSingleSampleWorkflow.unmapped_bam_suffix": ".bam",
"##_COMMENT3": "REFERENCES",
"PairedEndSingleSampleWorkflow.fingerprint_genotypes_file": "gs://dsde-data-na12878-public/NA12878.hg38.reference.fingerprint.vcf",
"PairedEndSingleSampleWorkflow.fingerprint_genotypes_index": "gs://dsde-data-na12878-public/NA12878.hg38.reference.fingerprint.vcf.idx",
"PairedEndSingleSampleWorkflow.contamination_sites_ud": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.contam.UD",
"PairedEndSingleSampleWorkflow.contamination_sites_bed": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.contam.bed",
"PairedEndSingleSampleWorkflow.contamination_sites_mu": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.contam.mu",
"PairedEndSingleSampleWorkflow.scattered_calling_intervals": ["gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0001_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0002_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0003_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0004_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0005_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0006_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0007_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0008_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0009_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0010_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0011_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0012_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0013_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0014_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0015_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0016_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0017_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0018_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0019_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0020_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0021_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0022_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0023_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0024_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0025_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0026_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0027_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0028_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0029_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0030_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0031_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0032_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0033_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0034_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0035_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0036_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0037_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0038_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0039_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0040_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0041_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0042_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0043_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0044_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0045_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0046_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0047_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0048_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0049_of_50/scattered.interval_list", "gs://gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0050_of_50/scattered.interval_list"],
"PairedEndSingleSampleWorkflow.wgs_calling_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.interval_list",
"PairedEndSingleSampleWorkflow.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
"PairedEndSingleSampleWorkflow.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
"PairedEndSingleSampleWorkflow.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
"PairedEndSingleSampleWorkflow.ref_alt": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.alt",
"PairedEndSingleSampleWorkflow.ref_sa": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.sa",
"PairedEndSingleSampleWorkflow.ref_amb": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.amb",
"PairedEndSingleSampleWorkflow.ref_bwt": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.bwt",
"PairedEndSingleSampleWorkflow.ref_ann": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.ann",
"PairedEndSingleSampleWorkflow.ref_pac": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.pac",
"PairedEndSingleSampleWorkflow.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"
],
"PairedEndSingleSampleWorkflow.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"
],
"PairedEndSingleSampleWorkflow.dbSNP_vcf": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf",
"PairedEndSingleSampleWorkflow.dbSNP_vcf_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx",
"PairedEndSingleSampleWorkflow.wgs_coverage_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/wgs_coverage_regions.hg38.interval_list",
"PairedEndSingleSampleWorkflow.wgs_evaluation_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/wgs_evaluation_regions.hg38.interval_list",
"##PairedEndSingleSampleWorkflow.haplotype_database_file": "String (optional)",
"##_COMMENT5": "DISK SIZES + MISC",
"PairedEndSingleSampleWorkflow.flowcell_small_disk": 100,
"PairedEndSingleSampleWorkflow.flowcell_medium_disk": 200,
"PairedEndSingleSampleWorkflow.agg_small_disk": 200,
"PairedEndSingleSampleWorkflow.agg_medium_disk": 300,
"PairedEndSingleSampleWorkflow.agg_large_disk": 400,
"PairedEndSingleSampleWorkflow.preemptible_tries": 3,
"PairedEndSingleSampleWorkflow.agg_preemptible_tries": 3,
"##_COMMENT6": "MISC",
"PairedEndSingleSampleWorkflow.break_bands_at_multiples_of": 1000000,
"PairedEndSingleSampleWorkflow.haplotype_scatter_count": 50
}