nl-wgs_wf/parameters.json at main · uclanelsonlab/nl-wgs_wf · GitHub

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{
    "bwa_docker": {
        "description": "Docker image for BWA-MEM2 and SAMtools"
    },
    "picard_docker": {
        "description": "Docker image for Picard"
    },
    "deepvariant_docker": {
        "description": "Docker image for DeepVariant"
    },
    "manta_docker": {
        "description": "Docker image for Manta"
    },
    "cnvpytor_docker": {
        "description": "Docker image for CNVpytor"
    },
    "samtools_docker": {
        "description": "Docker image for SAMtools"
    },
    "expansionhunter_docker": {
        "description": "Docker image for ExpansionHunter"
    },
    "expansionhunterdenovo_docker": {
        "description": "Docker image for ExpansionHunterDenovo"
    },
    "multiqc_docker": {
        "description": "Docker image for MultiQC"
    },
    "automap_docker": {
        "description": "Docker image for Automap"
    },
    "mosdepth_docker": {
        "description": "Docker image for Mosdepth"
    },
    "bcftools_docker": {
        "description": "Docker image for BCFtools"
    },
    "hapcut2_docker": {
        "description": "Docker image for Hapcut2"
    },
    "strling_docker": {
        "description": "Docker image for STRling"
    },
    "input_type": {
        "description": "Type of input data: fastq, bam, or cram"
    },
    "input_1": {
        "description": "Primary input file: FASTQ R1 (fastq), BAM file (bam), or CRAM file (cram)",
        "optional": false
    },
    "input_2": {
        "description": "Secondary input file: FASTQ R2 (fastq), BAM index .bai (bam), or CRAM index .crai (cram) - optional for bam/cram",
        "optional": false
    },
    "sample_name": {
        "description": "Sample name"
    },
    "fasta": {
        "description": "Reference genome fasta file"
    },
    "fai": {
        "description": "Reference genome fai file"
    },
    "dict": {
        "description": "Reference genome dictionary file (.dict)"
    },
    "fasta_0123": {
        "description": "Reference genome 0123 file"
    },
    "fasta_amb": {
        "description": "Reference genome amb file"
    },
    "fasta_ann": {
        "description": "Reference genome ann file"
    },
    "fasta_bwt": {
        "description": "Reference genome bwt file"
    },
    "fasta_str": {
        "description": "Reference genome STR index file for STRling analysis (.str)"
    },
    "variant_catalog": {
        "description": "Variant catalog file"
    },
    "min_anchor_mapq": {
        "description": "Minimum anchor mapq"
    },
    "max_irr_mapq": {
        "description": "Maximum irr mapq"
    },
    "fastp_docker": {
        "description": "Docker image for Fastp"
    },
    "qualimap_docker": {
        "description": "Docker image for Qualimap"
    },
    "genome": {
        "description": "Genome"
    },
    "ref_qc": {
        "description": "NA12878 reference genome QC files"
    },
    "mt_bed": {
        "description": "Mitochondrial genes BED file for mosdepth coverage analysis"
    },
    "run_manta": {
        "description": "Run Manta structural variant calling (true/false). Set to false to skip Manta analysis.",
        "optional": true
    }
}