deepvariant.wdl

version 1.0

# Copyright (c) 2018 Leiden University Medical Center
#
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task RunDeepVariant {
    input {
        File referenceFasta
        File referenceFastaIndex
        File inputBam
        File inputBamIndex
        String modelType
        String outputVcf
        String? postprocessVariantsExtraArgs
        File? customizedModel
        Int? numShards
        String? outputGVcf
        String? outputGVcfIndex
        File? regions
        String? sampleName
        Boolean? VCFStatsReport = true

        String memory = "3GiB"
        Int timeMinutes = 5000
        String dockerImage = "google/deepvariant:1.0.0"
    }

    command {
        set -e
        /opt/deepvariant/bin/run_deepvariant \
        --ref ~{referenceFasta} \
        --reads ~{inputBam} \
        --model_type ~{modelType} \
        --output_vcf ~{outputVcf} \
        ~{"--output_gvcf " + outputGVcf} \
        ~{"--customized_model " + customizedModel} \
        ~{"--num_shards " + numShards} \
        ~{"--regions "  + regions} \
        ~{"--sample_name " + sampleName} \
        ~{"--postprocess_variants_extra_args " + postprocessVariantsExtraArgs} \
        ~{true="--vcf_stats_report" false="--novcf_stats_report" VCFStatsReport}
    }

    runtime {
        memory: memory
        time_minutes: timeMinutes
        docker: dockerImage
    }

    output {
        File outputVCF = outputVcf
        File outputVCFIndex = outputVcf + ".tbi"
        Array[File] outputVCFStatsReport = glob("*.visual_report.html")
        File? outputGVCF = outputGVcf
        File? outputGVCFIndex = outputGVcfIndex
    }

    parameter_meta {
        # inputs
        referenceFasta: {description: "Genome reference to use.", category: "required"}
        referenceFastaIndex: {description: "Index for the genome reference file.", category: "required"}
        inputBam: {description: "Aligned, sorted, indexed BAM file containing the reads we want to call.", category: "required"}
        inputBamIndex: {description: "Index for the input bam file.", category: "required"}
        modelType: {description: "<WGS|WES|PACBIO>. Type of model to use for variant calling. Each model_type has an associated default model, which can be overridden by the --customized_model flag.", category: "required"}
        outputVcf: {description: "Path where we should write VCF file.", category: "required"}
        postprocessVariantsExtraArgs: {description: "A comma-separated list of flag_name=flag_value. 'flag_name' has to be valid flags for calpostprocess_variants.py.", category: "advanced"}
        customizedModel: {description: "A path to a model checkpoint to load for the `call_variants` step. If not set, the default for each --model_type will be used.", category: "advanced"}
        numShards: {description: "Number of shards for make_examples step.", category: "common"}
        outputGVcf: {description: "Path where we should write gVCF file.", category: "common"}
        outputGVcfIndex: {description: "Path to where the gVCF index file will be written. This is needed as a workaround, set it to `outputGVcf + '.tbi.'`", category: "common"}
        regions: {description: "List of regions we want to process, in BED/BEDPE format.", category: "advanced"}
        sampleName: {description: "Sample name to use instead of the sample name from the input reads BAM (SM tag in the header).", category: "common"}
        VCFStatsReport: {description: "Output a visual report (HTML) of statistics about the output VCF.", category: "common"}
        memory: {description: "The amount of memory this job will use.", category: "advanced"}
        timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
        dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}

        # outputs
        outputVCF: {description: "Output VCF file."}
        outputVCFIndex: {description: "Index of output VCF file."}
        outputVCFStatsReport: {description: "Statistics file."}
        outputGVCF: {description: "GVCF version of VCF file(s)."}
        outputGVCFIndex: {description: "Index of GVCF file(s)."}
    }
}