75 строки
5.4 KiB
JSON
75 строки
5.4 KiB
JSON
{
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"##_COMMENT1": "SAMPLE NAME AND UNMAPPED BAMS",
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"PreProcessingForVariantDiscovery_GATK4.sample_name": "NA12878",
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"PreProcessingForVariantDiscovery_GATK4.ref_name": "b37",
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"PreProcessingForVariantDiscovery_GATK4.flowcell_unmapped_bams_list": "https://datasettestinputs.blob.core.windows.net/dataset/gatk4-data-processing/NA12878_downsampled_for_testing/unmapped/NA12878_downsampled.txt",
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"PreProcessingForVariantDiscovery_GATK4.unmapped_bam_suffix": ".bam",
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"##_COMMENT2": "REFERENCE FILES",
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"PreProcessingForVariantDiscovery_GATK4.ref_dict": "https://datasettestinputs.blob.core.windows.net/dataset/references/b37/human_g1k_v37_decoy.dict",
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"PreProcessingForVariantDiscovery_GATK4.ref_fasta": "https://datasettestinputs.blob.core.windows.net/dataset/references/b37/human_g1k_v37_decoy.fasta",
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"PreProcessingForVariantDiscovery_GATK4.ref_fasta_index": "https://datasettestinputs.blob.core.windows.net/dataset/references/b37/human_g1k_v37_decoy.fasta.fai",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_sa": "https://datasettestinputs.blob.core.windows.net/dataset/references/b37/human_g1k_v37_decoy.fasta.sa",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_amb": "https://datasettestinputs.blob.core.windows.net/dataset/references/b37/human_g1k_v37_decoy.fasta.amb",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_bwt": "https://datasettestinputs.blob.core.windows.net/dataset/references/b37/human_g1k_v37_decoy.fasta.bwt",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_ann": "https://datasettestinputs.blob.core.windows.net/dataset/references/b37/human_g1k_v37_decoy.fasta.ann",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_pac": "https://datasettestinputs.blob.core.windows.net/dataset/references/b37/human_g1k_v37_decoy.fasta.pac",
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"##_COMMENT3": "KNOWN SITES RESOURCES",
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"PreProcessingForVariantDiscovery_GATK4.dbSNP_vcf": "https://datasettestinputs.blob.core.windows.net/dataset/references/b37/dbsnp_138.b37.vcf",
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"PreProcessingForVariantDiscovery_GATK4.dbSNP_vcf_index": "https://datasettestinputs.blob.core.windows.net/dataset/references/b37/dbsnp_138.b37.vcf.idx",
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"PreProcessingForVariantDiscovery_GATK4.known_indels_sites_VCFs": [
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"https://datasettestinputs.blob.core.windows.net/dataset/references/b37/Mills_and_1000G_gold_standard.indels.b37.vcf"
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],
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"PreProcessingForVariantDiscovery_GATK4.known_indels_sites_indices": [
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"https://datasettestinputs.blob.core.windows.net/dataset/references/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.idx"
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],
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"##_COMMENT4": "MISC PROGRAM PARAMETERS",
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"#PreProcessingForVariantDiscovery_GATK4.bwa_commandline_override": "String? (optional)",
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"PreProcessingForVariantDiscovery_GATK4.compression_level": 5,
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.num_cpu": "16",
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"##_COMMENT5": "DOCKERS",
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"#PreProcessingForVariantDiscovery_GATK4.gotc_docker_override": "String? (optional)",
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"#PreProcessingForVariantDiscovery_GATK4.gatk_docker_override": "String? (optional)",
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"#PreProcessingForVariantDiscovery_GATK4.python_docker_override": "String? (optional)",
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"##_COMMENT6": "PATHS",
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"#PreProcessingForVariantDiscovery_GATK4.gotc_path_override": "String? (optional)",
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"#PreProcessingForVariantDiscovery_GATK4.gatk_path_override": "String? (optional)",
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"##_COMMENT7": "JAVA OPTIONS",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.java_opt": "-Xms3000m",
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"PreProcessingForVariantDiscovery_GATK4.MergeBamAlignment.java_opt": "-Xms3000m",
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"PreProcessingForVariantDiscovery_GATK4.MarkDuplicates.java_opt": "-Xms4000m",
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"PreProcessingForVariantDiscovery_GATK4.SortAndFixTags.java_opt_sort": "-Xms4000m",
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"PreProcessingForVariantDiscovery_GATK4.SortAndFixTags.java_opt_fix": "-Xms500m",
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"PreProcessingForVariantDiscovery_GATK4.BaseRecalibrator.java_opt": "-Xms4000m",
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"PreProcessingForVariantDiscovery_GATK4.GatherBqsrReports.java_opt": "-Xms3000m",
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"PreProcessingForVariantDiscovery_GATK4.ApplyBQSR.java_opt": "-Xms3000m",
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"PreProcessingForVariantDiscovery_GATK4.GatherBamFiles.java_opt": "-Xms2000m",
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"##_COMMENT8": "MEMORY ALLOCATION",
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"PreProcessingForVariantDiscovery_GATK4.GetBwaVersion.mem_size": "1 GB",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.mem_size": "14 GB",
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"PreProcessingForVariantDiscovery_GATK4.MergeBamAlignment.mem_size": "3500 MB",
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"PreProcessingForVariantDiscovery_GATK4.MarkDuplicates.mem_size": "7 GB",
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"PreProcessingForVariantDiscovery_GATK4.SortAndFixTags.mem_size": "5000 MB",
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"PreProcessingForVariantDiscovery_GATK4.CreateSequenceGroupingTSV.mem_size": "2 GB",
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"PreProcessingForVariantDiscovery_GATK4.BaseRecalibrator.mem_size": "6 GB",
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"PreProcessingForVariantDiscovery_GATK4.GatherBqsrReports.mem_size": "3500 MB",
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"PreProcessingForVariantDiscovery_GATK4.ApplyBQSR.mem_size": "3500 MB",
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"PreProcessingForVariantDiscovery_GATK4.GatherBamFiles.mem_size": "3 GB",
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"##_COMMENT9": "DISK SIZE ALLOCATION",
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"PreProcessingForVariantDiscovery_GATK4.agg_small_disk": 200,
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"PreProcessingForVariantDiscovery_GATK4.agg_medium_disk": 300,
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"PreProcessingForVariantDiscovery_GATK4.agg_large_disk": 400,
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"PreProcessingForVariantDiscovery_GATK4.flowcell_small_disk": 100,
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"PreProcessingForVariantDiscovery_GATK4.flowcell_medium_disk": 200,
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"##_COMMENT10": "PREEMPTIBLES",
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"#PreProcessingForVariantDiscovery_GATK4.preemptible_tries_override": "Int? (optional)"
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}
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