stringtie.wdl

version 1.0

# Copyright (c) 2017 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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# SOFTWARE.

task Stringtie {
    input {
        File bam
        File bamIndex
        Boolean skipNovelTranscripts = false
        String assembledTranscriptsFile

        File? referenceGtf
        Boolean? firstStranded
        Boolean? secondStranded
        String? geneAbundanceFile
        Float? minimumCoverage

        Int threads = 1
        String memory = "2GiB"
        Int timeMinutes = 1 + ceil(size(bam, "G") * 60 / threads)
        String dockerImage = "quay.io/biocontainers/stringtie:1.3.6--h92e31bf_0"
    }

    command {
        set -e
        mkdir -p "$(dirname ~{assembledTranscriptsFile})"
        stringtie \
        ~{"-p " + threads} \
        ~{"-G " + referenceGtf} \
        ~{true="-e" false="" skipNovelTranscripts} \
        ~{true="--rf" false="" firstStranded} \
        ~{true="--fr" false="" secondStranded} \
        ~{"-c " + minimumCoverage} \
        -o ~{assembledTranscriptsFile} \
        ~{"-A " + geneAbundanceFile} \
        ~{bam}
    }

    output {
        File assembledTranscripts = assembledTranscriptsFile
        File? geneAbundance = geneAbundanceFile
    }

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

    parameter_meta {
        # inputs
        bam: {description: "The input BAM file.", category: "required"}
        bamIndex: {description: "The input BAM file's index.", category: "required"}
        skipNovelTranscripts: {description: "Whether new transcripts should be assembled or not.", category: "common"}
        assembledTranscriptsFile: {description: "Where the output of the assembly should be written.", category: "required"}
        referenceGtf: {description: "A reference GTF file to be used as guide.", category: "common"}
        firstStranded: {description: "Equivalent to the --rf flag of stringtie.", category: "required"}
        secondStranded: {description: "Equivalent to the --fr flag of stringtie.", category: "required"}
        geneAbundanceFile: {description: "Where the abundance file should be written.", category: "common"}
        minimumCoverage: {description: "The minimum coverage for a transcript to be shown in the output.", category: "advanced"}
        threads: {description: "The number of threads to use.", category: "advanced"}
        memory: {description: "The amount of memory needed for this task in GB.", 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
        assembledTranscripts: {description: "GTF file containing the assembled transcripts."}
        geneAbundance: {description: "Gene abundances in tab-delimited format."}
    }
}

task Merge {
    input {
        Array[File]+ gtfFiles
        String outputGtfPath
        Boolean keepMergedTranscriptsWithRetainedIntrons = false

        File? guideGtf
        Int? minimumLength
        Float? minimumCoverage
        Float? minimumFPKM
        Float? minimumTPM
        Float? minimumIsoformFraction
        String? label

        String memory = "10GiB"
        Int timeMinutes = 1 + ceil(size(gtfFiles, "G") * 20)
        String dockerImage = "quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0"
    }

    command {
        set -e
        mkdir -p "$(dirname ~{outputGtfPath})"
        stringtie --merge \
        -o ~{outputGtfPath} \
        ~{"-G " + guideGtf} \
        ~{"-m " + minimumLength } \
        ~{"-c " + minimumCoverage} \
        ~{"-F " + minimumFPKM} \
        ~{"-T " + minimumTPM} \
        ~{"-f " + minimumIsoformFraction} \
        ~{true="-i" false="" keepMergedTranscriptsWithRetainedIntrons} \
        ~{"-l " + label} \
        ~{sep=" " gtfFiles}
    }

    output {
        File mergedGtfFile = outputGtfPath
    }

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

    parameter_meta {
        # inputs
        gtfFiles: {description: "The GTF files produced by stringtie.", category: "required"}
        outputGtfPath: {description: "Where the output should be written.", category: "required"}
        keepMergedTranscriptsWithRetainedIntrons: {description: "Equivalent to the -i flag of 'stringtie --merge'.", category: "advanced"}
        guideGtf: {description: "Equivalent to the -G option of 'stringtie --merge'.", category: "advanced"}
        minimumLength: {description: "Equivalent to the -m option of 'stringtie --merge'.", category: "advanced"}
        minimumCoverage: {description: "Equivalent to the -c option of 'stringtie --merge'.", category: "advanced"}
        minimumFPKM: {description: "Equivalent to the -F option of 'stringtie --merge'.", category: "advanced"}
        minimumTPM: {description: "Equivalent to the -T option of 'stringtie --merge'.", category: "advanced"}
        minimumIsoformFraction: {description: "Equivalent to the -f option of 'stringtie --merge'.", category: "advanced"}
        label: {description: "Equivalent to the -l option of 'stringtie --merge'.", category: "advanced"}
        memory: {description: "The amount of memory needed for this task in GB.", 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
        mergedGtfFile: {description: "A merged GTF file from a set of GTF files."}
    }
}