clair3.wdl

version 1.0

# Copyright (c) 2024 Leiden University Medical Center
#
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# SOFTWARE.

task Clair3 {
    input {
        File bam 
        File bamIndex 
        File referenceFasta 
        File referenceFastaFai
        String outputPrefix 
        String? sampleName
        File? modelTar
        String? builtinModel
        String platform
        Int threads = 8
        Boolean includeAllCtgs = false
        String memory = "~{threads + 16}GiB"
        Int timeMinutes = 10 + ceil(size(bam, "G") * 200 / threads)
        String dockerImage = "quay.io/biocontainers/clair3:1.0.10--py39h46983ab_0"   
    }

    String modelArg = "~{if defined(modelTar) then basename(select_first([modelTar]), '.tar.gz') else builtinModel}"

    command <<<
        set -e
        ~{if defined(modelTar) then "tar -xvf " + modelTar else "" }
        mkdir -p $(dirname ~{outputPrefix})
        run_clair3.sh \
        --model=~{modelArg} \
        --ref_fn=~{referenceFasta} \
        --bam_fn=~{bam} \
        --output=out \
        --threads=~{threads} \
        --platform=~{platform} \
        ~{"--sample_name=" + sampleName} \
        ~{true="--include_all_ctgs" false ="" includeAllCtgs}  
        mv out/merge_output.vcf.gz ~{outputPrefix}.vcf.gz
        mv out/merge_output.vcf.gz.tbi ~{outputPrefix}.vcf.gz.tbi
    >>>

    output {
        File vcf = "~{outputPrefix}.vcf.gz"
        File vcfIndex = "~{outputPrefix}.vcf.gz.tbi"  
    }

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

    parameter_meta {
        # input
        bam: {description: "The input alignment file", category: "required"}
        bamIndex: {description: "The index for the input alignment file", category: "required"}
        referenceFasta: {description: "The reference fasta file.", category: "required"}
        referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
        outputPrefix: {description: "The output prefix where the data should be placed.", category: "common"}
        modelTar: {description: "The TAR file with the model", category: "common"}
        builtinModel: {description: "The builtin model name (in case a tar file is not used)", category: "common"}
        sampleName: {description: "The name of the sample in the VCF", category: "common"}
        platform: {description: "platform setting for clair3.", category: "required"}
        includeAllCtgs: {description: "whether or not to call all contigs in the reference", category: "advanced"}
        threads: {description: "The number of threads to use for variant calling.", category: "advanced"}
        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"}
    
        # output
        vcf: {description: "Output VCF file."}
        vcfIndex: {description: "Output VCF index."}

    }
}