{
    "theiacov_gc.pangolin_docker_image": "staphb/pangolin:3.1.3-pangolearn-2021-06-15",
    
    "theiacov_gc.theiacov_clearlabs.nextclade_one_sample.docker": "nextstrain/nextclade:0.14.4",
    "theiacov_gc.theiacov_illumina_pe.nextclade_one_sample.docker": "nextstrain/nextclade:0.14.4",
    "theiacov_gc.theiacov_illumina_se.nextclade_one_sample.docker": "nextstrain/nextclade:0.14.4",
    "theiacov_gc.theiacov_ont.nextclade_one_sample.docker": "nextstrain/nextclade:0.14.4",

    "theiacov_gc.theiacov_clearlabs.ncbi_scrub_se.docker": "ncbi/sra-human-scrubber:1.0.2021-05-05",
    "theiacov_gc.theiacov_illumina_pe.read_QC_trim.ncbi_scrub_pe.docker": "ncbi/sra-human-scrubber:1.0.2021-05-05",
    "theiacov_gc.theiacov_ont.ncbi_scrub_se.docker": "ncbi/sra-human-scrubber:1.0.2021-05-05",

    "theiacov_gc.theiacov_clearlabs.consensus.docker": "staphb/artic-ncov2019:1.3.0",
    "theiacov_gc.theiacov_ont.consensus.docker": "staphb/artic-ncov2019:1.3.0",

    "theiacov_gc.theiacov_illumina_pe.read_QC_trim.bbduk.docker": "staphb/bbtools:38.76",
    "theiacov_gc.theiacov_illumina_se.read_QC_trim.bbduk_se.docker": "staphb/bbtools:38.76",

    "theiacov_gc.theiacov_illumina_se.read_QC_trim.trimmomatic_se.docker": "staphb/trimmomatic:0.39",
    "theiacov_gc.theiacov_illumina_pe.read_QC_trim.trimmomatic.docker": "staphb/trimmomatic:0.39",

    "theiacov_gc.theiacov_clearlabs.vadr.docker": "staphb/vadr:1.2.1",
    "theiacov_gc.theiacov_illumina_pe.vadr.docker": "staphb/vadr:1.2.1",
    "theiacov_gc.theiacov_illumina_se.vadr.docker": "staphb/vadr:1.2.1",
    "theiacov_gc.theiacov_ont.vadr.docker": "staphb/vadr:1.2.1",

    "theiacov_gc.theiacov_clearlabs.consensus.cpu": 8,
    "theiacov_gc.theiacov_clearlabs.consensus.medaka_model": "r941_min_high_g360",
    "theiacov_gc.theiacov_clearlabs.kraken2_dehosted.cpus": 4,
    "theiacov_gc.theiacov_clearlabs.kraken2_raw.cpus": 4,
    "theiacov_gc.theiacov_clearlabs.normalise": 20000,
    "theiacov_gc.theiacov_clearlabs.pangolin3.inference_engine": "usher",
    "theiacov_gc.theiacov_clearlabs.pangolin3.max_ambig": 0.5,
    "theiacov_gc.theiacov_clearlabs.pangolin3.min_length": 10000,
    "theiacov_gc.theiacov_clearlabs.seq_method": "ONT via Clear Labs WGS",
    "theiacov_gc.theiacov_clearlabs.vadr.maxlen": 30000,
    "theiacov_gc.theiacov_clearlabs.vadr.minlen": 50,
    "theiacov_gc.theiacov_clearlabs.vadr.skip_length": 10000,
    "theiacov_gc.theiacov_clearlabs.vadr.vadr_opts": "--glsearch -s -r --nomisc --mkey sarscov2 --alt_fail lowscore,fstukcnf,insertnn,deletinn --mdir /opt/vadr/vadr-models/",

    "theiacov_gc.theiacov_illumina_pe.bwa.cpus": 6,
    "theiacov_gc.theiacov_illumina_pe.bwa.reference_genome": "/artic-ncov2019/primer_schemes/nCoV-2019/V3/nCoV-2019.reference.fasta",
    "theiacov_gc.theiacov_illumina_pe.consensus.char_unknown": "N",
    "theiacov_gc.theiacov_illumina_pe.consensus.count_orphans": true,
    "theiacov_gc.theiacov_illumina_pe.consensus.disable_baq": true,
    "theiacov_gc.theiacov_illumina_pe.consensus.max_depth": "600000",
    "theiacov_gc.theiacov_illumina_pe.consensus.min_bq": "0",
    "theiacov_gc.theiacov_illumina_pe.consensus.min_depth": "10",
    "theiacov_gc.theiacov_illumina_pe.consensus.min_freq": "0.6",
    "theiacov_gc.theiacov_illumina_pe.consensus.min_qual": "20",
    "theiacov_gc.theiacov_illumina_pe.consensus.ref_genome": "/artic-ncov2019/primer_schemes/nCoV-2019/V3/nCoV-2019.reference.fasta",
    "theiacov_gc.theiacov_illumina_pe.consensus.ref_gff": "/reference/GCF_009858895.2_ASM985889v3_genomic.gff",
    "theiacov_gc.theiacov_illumina_pe.pangolin3.inference_engine": "usher",
    "theiacov_gc.theiacov_illumina_pe.pangolin3.max_ambig": 0.5,
    "theiacov_gc.theiacov_illumina_pe.pangolin3.min_length": 10000,
    "theiacov_gc.theiacov_illumina_pe.primer_trim.keep_noprimer_reads": true,
    "theiacov_gc.theiacov_illumina_pe.read_QC_trim.kraken2_dehosted.cpus": 4,
    "theiacov_gc.theiacov_illumina_pe.read_QC_trim.kraken2_raw.cpus": 4,
    "theiacov_gc.theiacov_illumina_pe.read_QC_trim.trimmomatic.threads": 4,
    "theiacov_gc.theiacov_illumina_pe.read_QC_trim.trimmomatic_minlen": 75,
    "theiacov_gc.theiacov_illumina_pe.read_QC_trim.trimmomatic_quality_trim_score": 30,
    "theiacov_gc.theiacov_illumina_pe.read_QC_trim.trimmomatic_window_size": 4,
    "theiacov_gc.theiacov_illumina_pe.seq_method": "Illumina paired-end",
    "theiacov_gc.theiacov_illumina_pe.vadr.maxlen": 30000,
    "theiacov_gc.theiacov_illumina_pe.vadr.minlen": 50,
    "theiacov_gc.theiacov_illumina_pe.vadr.skip_length": 10000,
    "theiacov_gc.theiacov_illumina_pe.vadr.vadr_opts": "--glsearch -s -r --nomisc --mkey sarscov2 --alt_fail lowscore,fstukcnf,insertnn,deletinn --mdir /opt/vadr/vadr-models/",
    "theiacov_gc.theiacov_illumina_pe.variant_call.count_orphans": true,
    "theiacov_gc.theiacov_illumina_pe.variant_call.disable_baq": true,
    "theiacov_gc.theiacov_illumina_pe.variant_call.max_depth": "600000",
    "theiacov_gc.theiacov_illumina_pe.variant_call.min_bq": "0",
    "theiacov_gc.theiacov_illumina_pe.variant_call.min_depth": "10",
    "theiacov_gc.theiacov_illumina_pe.variant_call.min_freq": "0.6",
    "theiacov_gc.theiacov_illumina_pe.variant_call.min_qual": "20",
    "theiacov_gc.theiacov_illumina_pe.variant_call.ref_genome": "/artic-ncov2019/primer_schemes/nCoV-2019/V3/nCoV-2019.reference.fasta",
    "theiacov_gc.theiacov_illumina_pe.variant_call.ref_gff": "/reference/GCF_009858895.2_ASM985889v3_genomic.gff",

    "theiacov_gc.theiacov_illumina_se.bwa.cpus": 6,
    "theiacov_gc.theiacov_illumina_se.bwa.reference_genome": "/artic-ncov2019/primer_schemes/nCoV-2019/V3/nCoV-2019.reference.fasta",
    "theiacov_gc.theiacov_illumina_se.consensus.char_unknown": "N",
    "theiacov_gc.theiacov_illumina_se.consensus.count_orphans": true,
    "theiacov_gc.theiacov_illumina_se.consensus.disable_baq": true,
    "theiacov_gc.theiacov_illumina_se.consensus.max_depth": "600000",
    "theiacov_gc.theiacov_illumina_se.consensus.min_bq": "0",
    "theiacov_gc.theiacov_illumina_se.consensus.min_depth": "10",
    "theiacov_gc.theiacov_illumina_se.consensus.min_freq": "0.6",
    "theiacov_gc.theiacov_illumina_se.consensus.min_qual": "20",
    "theiacov_gc.theiacov_illumina_se.consensus.ref_genome": "/artic-ncov2019/primer_schemes/nCoV-2019/V3/nCoV-2019.reference.fasta",
    "theiacov_gc.theiacov_illumina_se.consensus.ref_gff": "/reference/GCF_009858895.2_ASM985889v3_genomic.gff",
    "theiacov_gc.theiacov_illumina_se.pangolin3.inference_engine": "usher",
    "theiacov_gc.theiacov_illumina_se.pangolin3.max_ambig": 0.5,
    "theiacov_gc.theiacov_illumina_se.pangolin3.min_length": 10000,
    "theiacov_gc.theiacov_illumina_se.primer_trim.keep_noprimer_reads": true,
    "theiacov_gc.theiacov_illumina_se.read_QC_trim.kraken2_raw.cpus": 4,
    "theiacov_gc.theiacov_illumina_se.read_QC_trim.trimmomatic_minlen": 25,
    "theiacov_gc.theiacov_illumina_se.read_QC_trim.trimmomatic_quality_trim_score": 30,
    "theiacov_gc.theiacov_illumina_se.read_QC_trim.trimmomatic_se.threads": 4,
    "theiacov_gc.theiacov_illumina_se.read_QC_trim.trimmomatic_window_size": 4,
    "theiacov_gc.theiacov_illumina_se.seq_method": "Illumina single-end",
    "theiacov_gc.theiacov_illumina_se.vadr.maxlen": 30000,
    "theiacov_gc.theiacov_illumina_se.vadr.minlen": 50,
    "theiacov_gc.theiacov_illumina_se.vadr.skip_length": 10000,
    "theiacov_gc.theiacov_illumina_se.vadr.vadr_opts": "--glsearch -s -r --nomisc --mkey sarscov2 --alt_fail lowscore,fstukcnf,insertnn,deletinn --mdir /opt/vadr/vadr-models/",
    "theiacov_gc.theiacov_illumina_se.variant_call.count_orphans": true,
    "theiacov_gc.theiacov_illumina_se.variant_call.disable_baq": true,
    "theiacov_gc.theiacov_illumina_se.variant_call.max_depth": "600000",
    "theiacov_gc.theiacov_illumina_se.variant_call.min_bq": "0",
    "theiacov_gc.theiacov_illumina_se.variant_call.min_depth": "10",
    "theiacov_gc.theiacov_illumina_se.variant_call.min_freq": "0.6",
    "theiacov_gc.theiacov_illumina_se.variant_call.min_qual": "20",
    "theiacov_gc.theiacov_illumina_se.variant_call.ref_genome": "/artic-ncov2019/primer_schemes/nCoV-2019/V3/nCoV-2019.reference.fasta",
    "theiacov_gc.theiacov_illumina_se.variant_call.ref_gff": "/reference/GCF_009858895.2_ASM985889v3_genomic.gff",

    "theiacov_gc.theiacov_ont.consensus.cpu": 8,
    "theiacov_gc.theiacov_ont.consensus.medaka_model": "r941_min_high_g360",
    "theiacov_gc.theiacov_ont.kraken2_dehosted.cpus": 4,
    "theiacov_gc.theiacov_ont.kraken2_raw.cpus": 4,
    "theiacov_gc.theiacov_ont.normalise": 200,
    "theiacov_gc.theiacov_ont.pangolin3.inference_engine": "usher",
    "theiacov_gc.theiacov_ont.pangolin3.max_ambig": 0.5,
    "theiacov_gc.theiacov_ont.pangolin3.min_length": 10000,
    "theiacov_gc.theiacov_ont.read_filtering.cpu": 8,
    "theiacov_gc.theiacov_ont.read_filtering.max_length": 700,
    "theiacov_gc.theiacov_ont.read_filtering.min_length": 400,
    "theiacov_gc.theiacov_ont.read_filtering.run_prefix": "artic_ncov2019",
    "theiacov_gc.theiacov_ont.seq_method": "ONT",
    "theiacov_gc.theiacov_ont.vadr.maxlen": 30000,
    "theiacov_gc.theiacov_ont.vadr.minlen": 50,
    "theiacov_gc.theiacov_ont.vadr.skip_length": 10000,
    "theiacov_gc.theiacov_ont.vadr.vadr_opts": "--glsearch -s -r --nomisc --mkey sarscov2 --alt_fail lowscore,fstukcnf,insertnn,deletinn --mdir /opt/vadr/vadr-models/"
}