sequence-classification.wdl

version 1.0

# Copyright (c) 2020 Leiden University Medical Center
#
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# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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import "sample.wdl" as sampleWorkflow
import "structs.wdl" as structs
import "tasks/biowdl.wdl" as biowdl
import "tasks/common.wdl" as common
import "tasks/multiqc.wdl" as multiqc

workflow Classification {
    input {
        File sampleConfigFile
        String outputDirectory = "."
        Boolean runQc = true

        File dockerImagesFile
    }

    meta {
        allowNestedInputs: true
    }

    call common.YamlToJson as convertDockerImagesFile {
        input:
            yaml = dockerImagesFile,
            outputJson = outputDirectory + "/dockerImages.json"
    }

    Map[String, String] dockerImages = read_json(convertDockerImagesFile.json)

    call biowdl.InputConverter as convertSampleConfig {
        input:
            samplesheet = sampleConfigFile,
            outputFile = outputDirectory + "/samplesheet.json",
            dockerImage = dockerImages["biowdl-input-converter"]
    }

    SampleConfig sampleConfig = read_json(convertSampleConfig.json)
    Array[Sample] allSamples = sampleConfig.samples

    scatter (sample in allSamples) {
        call sampleWorkflow.SampleWorkflow as sampleWorkflow {
            input:
                sample = sample,
                outputDirectory = outputDirectory + "/" + sample.id,
                runQc = runQc,
                dockerImages = dockerImages
        }
    }

    if (runQc) {
        call multiqc.MultiQC as multiqcTask {
            input:
                reports = flatten(sampleWorkflow.workflowReports),
                outDir = outputDirectory + "/multiqc",
                dataDir = true,
                dockerImage = dockerImages["multiqc"]
        }
    }

    output {
        File dockerImagesList = convertDockerImagesFile.json
        Array[File] workflowReports = flatten(sampleWorkflow.workflowReports)
        Array[File] centrifugeClassification = sampleWorkflow.centrifugeClassification
        Array[File] centrifugeReport = sampleWorkflow.centrifugeReport
        Array[File] centrifugeKReport = sampleWorkflow.centrifugeKReport
        Array[File] kronaPlot = sampleWorkflow.kronaPlot
        File? multiqcReport = multiqcTask.multiqcReport
        File? multiqcZip = multiqcTask.multiqcDataDirZip
    }

    parameter_meta {
        # inputs
        sampleConfigFile: {description: "Samplesheet describing input fasta/fastq files.", category: "required"}
        outputDirectory: {description: "The directory to which the outputs will be written.", category: "common"}
        runQc: {description: "Run the QC pipeline when the input is fastq.", category: "common"}
        dockerImagesFile: {description: "The docker image used for this workflow. Changing this may result in errors which the developers may choose not to address.", category: "required"}

        # outputs
        dockerImagesList: {description: "Json file describing the docker images used by the pipeline."}
        workflowReports: {description: "The qc workflow file(s)."}
        centrifugeClassification: {description: "File(s) with the classification results."}
        centrifugeReport: {description: "File(s) with a classification summary."}
        centrifugeKReport: {description: "File(s) with kraken style report(s)."}
        kronaPlot: {description: "Krona taxonomy plot file(s)."}
        multiqcReport: {description: "The multiqc file(s)."}
        multiqcZip: {description: "The multiqc data zip file(s)."}
    }
}