Candida-Phylo.inputs.json

{
    "CandidaPhylo.input_samples":[
        "C1", 
        "C4",
        "C6"],
    
    "CandidaPhylo.input_fastqs_1":[
        "FASTQ/C1_1.sample.fastq", 
        "FASTQ/C4_1.sample.fastq",
        "FASTQ/C6_1.sample.fastq"],
    
    "CandidaPhylo.input_fastqs_2":[
        "FASTQ/C1_2.sample.fastq", 
        "FASTQ/C4_2.sample.fastq",
        "FASTQ/C6_2.sample.fastq"],

    "CandidaPhylo.do_align":true,
    "CandidaPhylo.run_name":"test",
    "CandidaPhylo.indel_filter_expr":"QD < 2.0 || FS > 60.0 || MQ < 40.0",
    "CandidaPhylo.snp_filter_expr":"QD < 2.0 || FS > 60.0 || MQ < 40.0",

    "CandidaPhylo.ref":"SC5314.fna",
    "CandidaPhylo.ref_ann":"SC5314.fna.ann",
    "CandidaPhylo.ref_index":"SC5314.fna.fai",
    "CandidaPhylo.ref_amb":"SC5314.fna.amb",
    "CandidaPhylo.ref_sa":"SC5314.fna.sa",
    "CandidaPhylo.ref_bwt":"SC5314.fna.bwt",
    "CandidaPhylo.ref_dict":"SC5314.fna.dict",
    "CandidaPhylo.ref_pac":"SC5314.fna.pac",

    "CandidaPhylo.docker":"xiaoli2020/fungi-gatk3:v1.0",
    "CandidaPhylo.picard_path":"/opt/picard.jar",
    "CandidaPhylo.gatk_path":"/opt/GenomeAnalysisTK.jar",

    "CandidaPhylo.small_mem_size_gb":4,
    "CandidaPhylo.med_mem_size_gb":4,
    "CandidaPhylo.large_mem_size_gb":4,
    "CandidaPhylo.extra_large_mem_size_gb":4,

    "CandidaPhylo.disk_size":120,
    "CandidaPhylo.med_disk_size":250,
    "CandidaPhylo.large_disk_size":500,
    "CandidaPhylo.extra_large_disk_size":700

}