inputs_habrok.json

{
  "FastqToVariants.sampleJson": "/groups/umcg-pmb/tmp01/projects/hematopathology/Lymphoma/20230601_GenomeScan_105690/20230601_GenomeScan_105690_10589.json",
  "FastqToVariants.fastqcModule": "FastQC/0.11.9-Java-11",
  "FastqToVariants.trimgaloreModule": "Trim_Galore/0.6.10-GCCcore-11.3.0",
  "FastqToVariants.multiqcModule": "MultiQC/1.14-foss-2022a",
  "FastqToVariants.bwaModule": "BWA/0.7.17-GCCcore-11.3.0",
  "FastqToVariants.picardModule": "picard/2.25.1-Java-11",
  "FastqToVariants.gatkModule": "GATK/4.3.0.0-GCCcore-11.3.0-Java-11",
  "FastqToVariants.samtoolsModule": "SAMtools/1.16.1-GCC-11.3.0",
  "FastqToVariants.hmmcopyutilsModule": "hmmcopy_utils/5911bf69f1-foss-2022a",
  "FastqToVariants.referenceBwaIndex": {
    "fastaFile": "./data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta",
    "ambFile": "./data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.amb",
    "annFile": "./data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.ann",
    "bwtFile": "./data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.bwt",
    "pacFile": "./data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.pac",
    "saFile": "./data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.sa",
    "altFile":"./data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.alt"
  },
  "FastqToVariants.reference": {
    "fasta": "./data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta",
    "dict": "./data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dict",
    "fai": "./data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.fai"
  },
  "FastqToVariants.targetIntervalList": "./data/interval_lists/hg38/S31285117_SureSelectV7_Regions_hg38.interval_list",
  "FastqToVariants.targetScatter": 3,
  "FastqToVariants.runCutadapt": false,
  "FastqToVariants.read1Adapters": ["AGATCGGAAGAGC"],
  "FastqToVariants.read2Adapters": ["AGATCGGAAGAGC"],
  "FastqToVariants.dbsnp": {
    "file" : "./data/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.gz",
    "index" : "./data/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi" 
  },
  "FastqToVariants.knownSites": 
    [
      {
        "file": "./data/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz",
        "index": "./data/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi"
      },
      {
        "file": "./data/gcp-public-data--broad-references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
        "index": "./data/gcp-public-data--broad-references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi"
      }
      
    ]
}