genome_example.json

{
    "INPUT_HAPLOID_FILE": {
        "path": "Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz", 
        "class": "File"
    }, 
    "HAPOLID_COPY_NAME": "Homo_sapiens.GRCh37.75.dna.primary_assembly.fa2.gz",
    "INPUT_VCF_FILE1": {
        "path": "", 
        "class": "File"
    },  
    "INPUT_VCF_FILE2": {
        "path": "", 
        "class": "File"
    },  
    "VARIANT_HAPLOID_FILE1": "test_haploid1.fasta",
    "VARIANT_HAPLOID_FILE2": "test_haploid2.fasta",
    "SED_STRING1": "s/>\\([[:graph:]]*\\)\\s/>\\1-hap1 /g",
    "SED_STRING2": "s/>\\([[:graph:]]*\\)\\s/>\\1-hap2 /g",
    "INPUT_GTF_FILE": {
        "path": "Homo_sapiens.GRCh37.75.gtf", 
        "class": "File"
    },
    "GTF_SUFFIX_STRING1": "hap1",
    "GTF_SUFFIX_STRING2": "hap2",
    "REF_NAME": "GRCH37_diploid",
    "NUM_CORES": 1
}