nl-wgs_wf/run_parameters_t2t.json at main · uclanelsonlab/nl-wgs_wf · GitHub

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{
    "bwa_docker": "224597534425.dkr.ecr.us-west-2.amazonaws.com/bwa-mem2:2.3_samtools-1.22",
    "picard_docker": "224597534425.dkr.ecr.us-west-2.amazonaws.com/picard:latest",
    "deepvariant_docker": "224597534425.dkr.ecr.us-west-2.amazonaws.com/deepvariant:1.9.0",
    "manta_docker": "224597534425.dkr.ecr.us-west-2.amazonaws.com/manta:1.6.0--h9ee0642_2",
    "cnvpytor_docker": "224597534425.dkr.ecr.us-west-2.amazonaws.com/cnvpytor:1.3.1--pyhdfd78af_0",
    "expansionhunter_docker": "224597534425.dkr.ecr.us-west-2.amazonaws.com/expansionhunter:5.0.0--hf366f20_1",
    "expansionhunterdenovo_docker": "224597534425.dkr.ecr.us-west-2.amazonaws.com/expansionhunterdenovo:0.9.0--hd6d6fdc_9",
    "multiqc_docker": "224597534425.dkr.ecr.us-west-2.amazonaws.com/multiqc:1.30--pyhdfd78af_0",
    "qualimap_docker": "224597534425.dkr.ecr.us-west-2.amazonaws.com/qualimap:2.3--hdfd78af_0",
    "fastp_docker": "224597534425.dkr.ecr.us-west-2.amazonaws.com/fastp:1.0.1--heae3180_0",
    "automap_docker": "224597534425.dkr.ecr.us-west-2.amazonaws.com/automap:v1.3",
    "samtools_docker": "224597534425.dkr.ecr.us-west-2.amazonaws.com/samtools:1.19.2--h50ea8bc_1",
    "mosdepth_docker": "224597534425.dkr.ecr.us-west-2.amazonaws.com/mosdepth:0.3.1--h4dc83fb_1",
    "hapcut2_docker": "224597534425.dkr.ecr.us-west-2.amazonaws.com/hapcut2:1.3.4--h7e4f606_2",
    "bcftools_docker": "224597534425.dkr.ecr.us-west-2.amazonaws.com/bcftools:v1.9-1-deb_cv1",
    "strling_docker": "224597534425.dkr.ecr.us-west-2.amazonaws.com/strling:0.5.2--hbbffb53_1",
    "fasta": "s3://ucla-rare-diseases/UCLA-UDN/assets/reference/T2T/chm13v2.0.fa",
    "fai": "s3://ucla-rare-diseases/UCLA-UDN/assets/reference/T2T/chm13v2.0.fa.fai",
    "dict": "s3://ucla-rare-diseases/UCLA-UDN/assets/reference/T2T/chm13v2.0.dict",
    "fasta_0123": "s3://ucla-rare-diseases/UCLA-UDN/assets/reference/T2T/chm13v2.0.fa.0123",
    "fasta_amb": "s3://ucla-rare-diseases/UCLA-UDN/assets/reference/T2T/chm13v2.0.fa.amb",
    "fasta_ann": "s3://ucla-rare-diseases/UCLA-UDN/assets/reference/T2T/chm13v2.0.fa.ann",
    "fasta_bwt": "s3://ucla-rare-diseases/UCLA-UDN/assets/reference/T2T/chm13v2.0.fa.bwt.2bit.64",
    "fasta_pac": "s3://ucla-rare-diseases/UCLA-UDN/assets/reference/T2T/chm13v2.0.fa.pac",
    "fasta_str": "s3://ucla-rare-diseases/UCLA-UDN/assets/reference/T2T/chm13v2.0.str",
    "input_1": "s3://ucla-rare-diseases/aws-healthomics-pipelines/assets/test-data/NA12878_30x_dna/ERR3239334_1.20.fastq.gz",
    "input_2": "s3://ucla-rare-diseases/aws-healthomics-pipelines/assets/test-data/NA12878_30x_dna/ERR3239334_2.20.fastq.gz",
    "sample_name": "NA12878_20pct",
    "variant_catalog": "s3://ucla-rare-diseases/aws-healthomics-pipelines/assets/expansionhunter/hg38/variant_catalog.json",
    "min_anchor_mapq": 50,
    "max_irr_mapq": 40,
    "genome": "hg38",
    "ref_qc": "s3://ucla-rare-diseases/aws-healthomics-pipelines/assets/references/NA12878_qc.tar.gz",
    "input_type": "fastq",
    "mt_bed": "s3://ucla-rare-diseases/UCLA-UDN/assets/reference/MT_hg38.bed"
}