biopet.wdl

task FastqSplitter {
    String? preCommand
    File inputFastq
    String outputPath
    Int numberChunks
    String tool_jar
    Array[Int] chunks = range(numberChunks)

    command {
        set -e -o pipefail
        ${preCommand}
        mkdir -p ${sep=' ' prefix(outputPath + "/chunk_", chunks)}
        if [ ${numberChunks} -gt 1 ]; then
            SEP="/${basename(inputFastq)} -o "
            java -jar ${tool_jar} -I ${inputFastq} -o ${sep='$SEP' prefix(outputPath + "/chunk_", chunks)}/${basename(inputFastq)}
        else
            ln -sf ${inputFastq} ${outputPath}/chunk_0/${basename(inputFastq)}
        fi
    }

    output {
        Array[File] outputFastqFiles = glob(outputPath + "/chunk_*/" + basename(inputFastq))
    }
}

task ScatterRegions {
    String? preCommand
    File ref_fasta
    File ref_dict
    String outputDirPath
    String tool_jar
    Int? scatterSize
    File? regions

    command {
        set -e -o pipefail
        ${preCommand}
        mkdir -p ${outputDirPath}
        java -Xmx2G -jar ${tool_jar} \
          -R ${ref_fasta} \
          -o ${outputDirPath} \
          ${"-s " + scatterSize} \
          ${"-L " + regions}
    }

    output {
        Array[File] scatters = glob(outputDirPath + "/scatter-*.bed")
    }
}

task SampleConfig {
    String? preCommand
    String tool_jar
    Array[File]+ inputFiles
    String? sample
    String? library
    String? readgroup
    String? jsonOutputPath
    String? tsvOutputPath

    command {
        set -e -o pipefail
        ${preCommand}
        mkdir -p . ${"$(dirname " + jsonOutputPath + ")"} ${"$(dirname " + tsvOutputPath + ")"}
        java -Xmx2G -jar ${tool_jar} \
        -i ${sep="-i " inputFiles} \
        ${"--sample " + sample} \
        ${"--library " + library} \
        ${"--readgroup " + readgroup} \
        ${"--jsonOutput " + jsonOutputPath} \
        ${"--tsvOutput " + tsvOutputPath}
    }

    output {
        Array[String] keys = read_lines(stdout())
        File? jsonOutput = jsonOutputPath
        File? tsvOutput = tsvOutputPath
        Object values = if (defined(tsvOutput) && size(tsvOutput) > 0) then read_map(tsvOutput) else { "": "" }
    }
}

task BaseCounter {
    String? preCommand
    String tool_jar #Should this be of type File?
    File bam
    File refFlat
    String outputDir
    String prefix

    command {
        set -e -o pipefail
        ${preCommand}
        mkdir -p ${outputDir}
        java -jar ${tool_jar} \
        -b ${bam} \
        -r ${refFlat} \
        -o ${outputDir} \
        -p ${prefix}
    }

    output {
        File exonAntisense = outputDir + "/" + prefix + ".base.exon.antisense.counts"
        File exon = outputDir + "/" + prefix + ".base.exon.counts"
        File exonMergeAntisense = outputDir + "/" + prefix + ".base.exon.merge.antisense.counts"
        File exonMerge = outputDir + "/" + prefix + ".base.exon.merge.counts"
        File exonMergeSense = outputDir + "/" + prefix + ".base.exon.merge.sense.counts"
        File exonSense = outputDir + "/" + prefix + ".base.exon.sense.counts"
        File geneAntisense = outputDir + "/" + prefix + ".base.gene.antisense.counts"
        File gene = outputDir + "/" + prefix + ".base.gene.counts"
        File geneExonicAntisense = outputDir + "/" + prefix + ".base.gene.exonic.antisense.counts"
        File geneExonic = outputDir + "/" + prefix + ".base.gene.exonic.counts"
        File geneExonicSense = outputDir + "/" + prefix + ".base.gene.exonic.sense.counts"
        File geneIntronicAntisense = outputDir + "/" + prefix + ".base.gene.intronic.antisense.counts"
        File geneIntronic = outputDir + "/" + prefix + ".base.gene.intronic.counts"
        File geneIntronicSense = outputDir + "/" + prefix + ".base.gene.intronic.sense.counts"
        File geneSense = outputDir + "/" + prefix + ".base.gene.sense.counts"
        File intronAntisense = outputDir + "/" + prefix + ".base.intron.antisense.counts"
        File intron = outputDir + "/" + prefix + ".base.intron.counts"
        File intronMergeAntisense = outputDir + "/" + prefix + ".base.intron.merge.antisense.counts"
        File intronMerge = outputDir + "/" + prefix + ".base.intron.merge.counts"
        File intronMergeSense = outputDir + "/" + prefix + ".base.intron.merge.sense.counts"
        File intronSense = outputDir + "/" + prefix + ".base.intron.sense.counts"
        File metaExonsNonStranded = outputDir + "/" + prefix + ".base.metaexons.non_stranded.counts"
        File metaExonsStrandedAntisense = outputDir + "/" + prefix + ".base.metaexons.stranded.antisense.counts"
        File metaExonsStranded = outputDir + "/" + prefix + ".base.metaexons.stranded.counts"
        File metaExonsStrandedSense = outputDir + "/" + prefix + ".base.metaexons.stranded.sense.counts"
        File transcriptAntisense = outputDir + "/" + prefix + ".base.transcript.antisense.counts"
        File transcript = outputDir + "/" + prefix + ".base.transcript.counts"
        File transcriptExonicAntisense = outputDir + "/" + prefix + ".base.transcript.exonic.antisense.counts"
        File transcriptExonic = outputDir + "/" + prefix + ".base.transcript.exonic.counts"
        File transcriptExonicSense = outputDir + "/" + prefix + ".base.transcript.exonic.sense.counts"
        File transcriptIntronicAntisense = outputDir + "/" + prefix + ".base.transcript.intronic.antisense.counts"
        File transcriptIntronic = outputDir + "/" + prefix + ".base.transcript.intronic.counts"
        File transcriptIntronicSense = outputDir + "/" + prefix + ".base.transcript.intronic.sense.counts"
        File transcriptSense = outputDir + "/" + prefix + ".base.transcript.sense.counts"
    }

    runtime {
        memory: 16
    }
}