faster_alternative_workflow.inputs.json

{
  "##_COMMENT1": "INPUT SAMPLES",
  "FasterAltWorkflow.input1_fq": "/cluster_share/data/gold_workflow/HG02769_1.fq",
  "FasterAltWorkflow.input2_fq": "/cluster_share/data/gold_workflow/HG02769_2.fq",
  "FasterAltWorkflow.sample": "NA12878",
  "FasterAltWorkflow.output_bam_basename": "NA12878",
  "FasterAltWorkflow.vcf_basename": "NA12878",

  "##_COMMENT2": "REFERENCE FILES",
  "FasterAltWorkflow.ref_dict": "/cluster_share/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dict",
  "FasterAltWorkflow.ref_fasta": "/cluster_share/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta",
  "FasterAltWorkflow.ref_fasta_index": "/cluster_share/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
  "FasterAltWorkflow.ref_alt": "/cluster_share/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.alt",
  "FasterAltWorkflow.ref_sa": "/cluster_share/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.sa",
  "FasterAltWorkflow.ref_amb": "/cluster_share/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.amb",
  "FasterAltWorkflow.ref_bwt": "/cluster_share/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.bwt",
  "FasterAltWorkflow.ref_ann": "/cluster_share/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.ann",
  "FasterAltWorkflow.ref_pac": "/cluster_share/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.pac",
  "FasterAltWorkflow.ref_mmi": "/cluster_share/Hybrid_Pipeline/tools/minimap2/Homo_sapiens_assembly38.mmi",
  "FasterAltWorkflow.wgs_calling_interval_list": "/cluster_share/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/wgs_calling_regions.hg38.interval_list",
  "FasterAltWorkflow.haplotype_scatter_count" : 56,
  "FasterAltWorkflow.break_bands_at_multiples_of" : 1000000,

  "##_COMMENT3": "RUNTIME CONFIG - If using Sambamba, set first and second value to 64GB and 80GB",
  "##_COMMENT3_1": "RUNTIME CONFIG - If using Samtools sort, set first and second value to 2G and 120GB",
  "##_COMMENT3_2": "The thread values below are set based on a node having 56 cores, and 256GB of memory, please modify as necessary",
  "##_COMMENT3_4": "For Haplotype Caller to use the FPGA - Change gatk_gkl_pairhmm_implementation to EXPERIMENTAL_FPGA_LOGLESS_CACHING",
  "FasterAltWorkflow.BamMapMarkSort.sort_memory": "64GB",
  "FasterAltWorkflow.BamMapMarkSort.memory": "80GB",
  "FasterAltWorkflow.ScatterIntervalList.memory":"12GB",
  "FasterAltWorkflow.HaplotypeCaller.memory":"6GB",
  "FasterAltWorkflow.GatherHC.memory":"3GB",
  "FasterAltWorkflow.BamMapMarkSort.cores": 56,
  "FasterAltWorkflow.BamMapMarkSort.cpu": 56,
  "FasterAltWorkflow.ScatterIntervalList.cpu":1,
  "FasterAltWorkflow.HaplotypeCaller.cpu":1,
  "FasterAltWorkflow.GatherHC.cpu":1,
  "FasterAltWorkflow.BamMapMarkSort.bwa_options": "mem -K 2500000 -v 3 -t 54 -Y -R'@RG\\tID:${sample}_${cores}T\\tLB:${sample}\\tSM:${sample}\\tPL:ILLUMINA' ${ref_fasta}",
  "FasterAltWorkflow.BamMapMarkSort.minimap2_options": "-t 54 -ax sr -R'@RG\\tID:${sample}_${cores}T\\tLB:${sample}\\tSM:${sample}\\tPL:ILLUMINA'",
  "FasterAltWorkflow.compression_level": 1,
  "FasterAltWorkflow.HaplotypeCaller.gatk_gkl_pairhmm_implementation": "AVX_LOGLESS_CACHING",
  "FasterAltWorkflow.HaplotypeCaller.gatk_gkl_pairhmm_threads": 1,
  "FasterAltWorkflow.HaplotypeCaller.smith_waterman_implementation": "AVX_ENABLED",
  "FasterAltWorkflow.BamMapMarkSort.tmpDir": "/mnt/app_nvm0/",

  "##_COMMENT4": "BINARY TOOL PATH",
  "FasterAltWorkflow.tool_path": "/cluster_share/Hybrid_Pipeline/tools"
}