Add deeptools

software/deeptools/computematrix/functions.nf

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+../../lib/functions.nf

software/deeptools/computematrix/main.nf

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+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process DEEPTOOLS_COMPUTEMATRIX {
+    tag "$meta.id"
+    label 'process_high'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    container "quay.io/biocontainers/deeptools:3.4.3--py_0"
+    //container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0"
+
+    conda (params.conda ? "bioconda::deeptools=3.4.3" : null)
+
+    input:
+    tuple val(meta), path(bigwig)
+    path bed
+    val options
+
+    output:
+    tuple val(meta), path("*.mat.gz"), emit: matrix
+    tuple val(meta), path("*.mat.tab"), emit: table
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    """
+    computeMatrix \\
+        $ioptions.args \\
+        --regionsFileName $bed \\
+        --scoreFileName $bigwig \\
+        --outFileName ${prefix}.computeMatrix.mat.gz \\
+        --outFileNameMatrix ${prefix}.computeMatrix.vals.mat.tab \\
+        --numberOfProcessors $task.cpus
+
+    computeMatrix --version | sed -e "s/computeMatrix //g" > ${software}.version.txt
+    """
+}

software/deeptools/plotfingerprint/functions.nf

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+../../lib/functions.nf

software/deeptools/plotfingerprint/main.nf

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+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process DEEPTOOLS_PLOTFINGERPRINT {
+    tag "$meta.id"
+    label 'process_high'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    container "quay.io/biocontainers/deeptools:3.4.3--py_0"
+    //container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0"
+
+    conda (params.conda ? "bioconda::deeptools=3.4.3" : null)
+
+    input:
+    tuple val(meta), path(bams), path(bais)
+    val options
+
+    output:
+    tuple val(meta), path("*.pdf"), emit: pdf
+    tuple val(meta), path("*.raw.txt"), emit: matrix
+    tuple val(meta), path("*.qcmetrics.txt"), emit: metrics
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    def extend   = (meta.single_end && params.fragment_size > 0) ? "--extendReads ${params.fragment_size}" : ''
+    """
+    plotFingerprint \\
+        $ioptions.args \\
+        $extend \\
+        --bamfiles ${bams.join(' ')} \\
+        --plotFile ${prefix}.plotFingerprint.pdf \\
+        --outRawCounts ${prefix}.plotFingerprint.raw.txt \\
+        --outQualityMetrics ${prefix}.plotFingerprint.qcmetrics.txt \\
+        --numberOfProcessors $task.cpus
+
+    plotFingerprint --version | sed -e "s/plotFingerprint //g" > ${software}.version.txt
+    """
+}

software/deeptools/plotheatmap/functions.nf

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+../../lib/functions.nf

software/deeptools/plotheatmap/main.nf

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+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process DEEPTOOLS_PLOTHEATMAP {
+    tag "$meta.id"
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    container "quay.io/biocontainers/deeptools:3.4.3--py_0"
+    //container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0"
+
+    conda (params.conda ? "bioconda::deeptools=3.4.3" : null)
+
+    input:
+    tuple val(meta), path(matrix)
+    val options
+
+    output:
+    tuple val(meta), path("*.pdf"), emit: pdf
+    tuple val(meta), path("*.tab"), emit: table
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    """
+    plotHeatmap \\
+        $ioptions.args \\
+        --matrixFile $matrix \\
+        --outFileName ${prefix}.plotHeatmap.pdf \\
+        --outFileNameMatrix ${prefix}.plotHeatmap.mat.tab
+
+    plotHeatmap --version | sed -e "s/plotHeatmap //g" > ${software}.version.txt
+    """
+}

software/deeptools/plotprofile/functions.nf

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+../../lib/functions.nf

software/deeptools/plotprofile/main.nf

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+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process DEEPTOOLS_PLOTPROFILE {
+    tag "$meta.id"
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    container "quay.io/biocontainers/deeptools:3.4.3--py_0"
+    //container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0"
+
+    conda (params.conda ? "bioconda::deeptools=3.4.3" : null)
+
+    input:
+    tuple val(meta), path(matrix)
+    val options
+
+    output:
+    tuple val(meta), path("*.pdf"), emit: pdf
+    tuple val(meta), path("*.tab"), emit: table
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    """
+    plotProfile \\
+        $ioptions.args \\
+        --matrixFile $matrix \\
+        --outFileName ${prefix}.plotProfile.pdf \\
+        --outFileNameData ${prefix}.plotProfile.tab
+
+    plotProfile --version | sed -e "s/plotProfile //g" > ${software}.version.txt
+    """
+}