Merge pull request #53 from drpatelh/master

Add in chipseq modules

deprecated/bwa-mem2/index/meta.yml

@@ -15,12 +15,12 @@ input:
         - input:
             type: file
             description: Input fasta file
-            pattern: *.{fasta,fa}
+            pattern: "*.{fasta,fa}"
 output:
     -
         - index:
             type: file
             description: bwa indexes file
-            pattern: *.{fasta,fa}.{amb,ann,bwt,pac,sa}
+            pattern: "*.{fasta,fa}.{amb,ann,bwt,pac,sa}"
 authors:
-    - @maxulysse
+    - "@maxulysse"

deprecated/bwa/index/main.nf

@@ -1,16 +0,0 @@
-process bwa_index {
-    tag "$fasta"
-
-    container 'quay.io/biocontainers/bwa:0.7.17--hed695b0_7'
-
-    input:
-        path fasta
-
-    output:
-        path "${fasta}.*"
-
-    script:
-    """
-    bwa index ${fasta}
-    """
-}

deprecated/bwa/mem/Dockerfile

@@ -1,7 +0,0 @@
-FROM nfcore/base
-LABEL authors="Jeremy Guntoro" \
-    description="Docker image containing all requirements for nf-core/modules/bwa/mem module"
-
-COPY environment.yml /
-RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-bwa-mem/bin:$PATH

deprecated/bwa/mem/environment.yml

@@ -1,10 +0,0 @@
-# You can use this file to create a conda environment for this pipeline:
-#   conda env create -f environment.yml
-name: nf-core-bwa-mem
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - bioconda::bwa=0.7.17
-  - bioconda::samtools=1.9

deprecated/bwa/mem/main.nf

@@ -1,27 +0,0 @@
-params.bwa_options = "-M -B 2"
-params.sequencer = "ILLUMINA"
-
-process bwa_mem {
-    tag "$id"
-
-    publishDir "${params.outdir}/bwa_mem", mode: 'copy'
-
-    //TO-DO: Change container declaration, for now a test container is present in my personal docker acccount
-    container 'jeremy1805/bwa-mem-img'
-
-    input:
-        tuple val(id), path(reads)
-        path genomeindex
-        val indexprefix
-
-    output:
-        tuple path("*.bam"), path("*.bai")
-
-    script:
-    """
-    bwa mem -t ${task.cpus} -R "@RG\\tID:${id}\\tLB:${id}\\tSM:${id}\\tPL:${params.sequencer}" \\
-    ${params.bwa_options} ${indexprefix} ${reads} | samtools sort -@8 -O BAM -o ${id}.bam -
-
-    samtools index ${id}.bam
-    """
-}

deprecated/samtools/Dockerfile

@@ -1,8 +0,0 @@
-FROM nfcore/base:1.7
-LABEL authors="phil.ewels@scilifelab.se" \
-    description="Docker image for nf-core modules samtools"
-
-# foobar
-COPY environment.yml /
-RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-modules-samtools/bin:$PATH

deprecated/samtools/environment.yml

@@ -1,9 +0,0 @@
-# You can use this file to create a conda environment for this pipeline:
-#   conda env create -f environment.yml
-name: nf-core-modules-samtools
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - samtools=1.9

deprecated/samtools/index/main.nf

@@ -1,21 +0,0 @@
-process samtools_index {
-    tag "${bam.baseName}"
-
-    container 'quay.io/biocontainers/samtools:1.9--h10a08f8_12'
-
-    input:
-    path bam
-
-    output:
-    path "*.bai"
-
-    script:
-    def suff_mem = ("${(task.memory.toBytes() - 6000000000) / task.cpus}" > 2000000000) ? 'true' : 'false'
-    def avail_mem = (task.memory && suff_mem) ? "-m" + "${(task.memory.toBytes() - 6000000000) / task.cpus}" : ''
-    """
-    samtools index $bam \\
-        -@ ${task.cpus} ${avail_mem}
-
-    samtools --version &> v_samtools.txt
-    """
-}

deprecated/samtools/sort/main.nf

@@ -1,18 +0,0 @@
-process samtools_index {
-    tag "${bam.baseName}"
-
-    container 'quay.io/biocontainers/samtools:1.9--h10a08f8_12'
-
-    input:
-    path bam
-
-    output:
-    path "*.bam.bai"
-
-    script:
-    """
-    samtools index $bam
-
-    samtools --version &> v_samtools.txt
-    """
-}

deprecated/trim_galore/Dockerfile

@@ -1,10 +0,0 @@
-FROM nfcore/base:1.7
-LABEL authors="phil.ewels@scilifelab.se" \
-    description="Docker image for nf-core modules trimgalore"
-
-#### THIS IS  A BUG
-
-# foobar
-COPY environment.yml /
-RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-modules-trimgalore/bin:$PATH

deprecated/trim_galore/environment.yml

@@ -1,9 +0,0 @@
-# You can use this file to create a conda environment for this pipeline:
-#   conda env create -f environment.yml
-name: nf-core-modules-trimgalore
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - trim-galore=0.6.4

deprecated/trim_galore/main.nf

@@ -1,102 +0,0 @@
-nextflow.preview.dsl=2
-
-params.singlecell = ''
-params.rrbs       = ''
-params.pbat       = ''
-params.single_end  = false
-
-params.trim_nextseq = 0
-
-params.clip_r1 = 0
-params.clip_r2 = 0
-params.three_prime_clip_r1 = 0
-params.three_prime_clip_r2 = 0
-
-
-process TRIM_GALORE {
-
-    // container 'quay.io/biocontainers/trim-galore:0.6.5--0' // maybe later
-    // tag "$sample_id"
-
-
-    // Trimming reports are not generated for e.g. --hardtrim5, --clock etc
-    // saveAs: {filename ->
-    //   else if (filename.indexOf("trimming_report.txt") > 0) "logs/$filename"
-    //   else filename
-    // }
-
-    publishDir "${outdir}/trim_galore",
-        mode: "copy", overwrite: true
-
-    input:
-        tuple val(name), path(reads)
-        val outdir
-        val trim_galore_args
-        val verbose
-
-    output:
-        tuple val(name), path ("*fq.gz"),             emit: reads
-        path "*trimming_report.txt", optional: true,  emit: report
-
-
-    script:
-        if (verbose){
-            println ("[MODULE] TRIM GALORE ARGS: " + trim_galore_args)
-        }
-
-        trim_galore_args += " --gzip "           // we like small files
-
-        pairedString = 0
-        if (reads instanceof List) {
-            pairedString = 1
-            trim_galore_args += " --paired "
-        }
-
-        if (params.clip_r1 > 0){
-            trim_galore_args += " --clip_r1 ${params.clip_r1} "
-        }
-        if (params.clip_r2 > 0){
-            trim_galore_args += " --clip_r2 ${params.clip_r2} "
-        }
-        if (params.three_prime_clip_r1> 0){
-            trim_galore_args += " --three_prime_clip_r1 ${params.three_prime_clip_r1} "
-        }
-        if (params.three_prime_clip_r2 > 0){
-            trim_galore_args += " --three_prime_clip_r2 ${params.three_prime_clip_r2} "
-        }
-
-        if (params.trim_nextseq > 0){
-            trim_galore_args += " --nextseq ${params.trim_nextseq} "
-        }
-
-
-        // Pre-set parameters for certain bisulfite-seq applications
-        if (params.singlecell){
-            trim_galore_args += " --clip_r1 6 "
-            if (pairedString == 1){
-                trim_galore_args += " --clip_r2 6 "
-            }
-        }
-        if (params.rrbs){
-            trim_galore_args += " --rrbs "
-        }
-        if  (params.pbat){
-            trim_galore_args += " --clip_r1 $params.pbat "
-            if (pairedString == 1){
-                trim_galore_args += " --clip_r2 $params.pbat "
-            }
-        }
-
-        """
-        module load trim_galore
-        trim_galore $trim_galore_args $reads
-        """
-
-}
-
-
-
-
-
-
-

software/bwa/index/functions.nf

@@ -0,0 +1 @@
+../../lib/functions.nf

software/bwa/index/main.nf

@@ -0,0 +1,31 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process BWA_INDEX {
+    tag "$fasta"
+    label 'process_high'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+
+    container "biocontainers/bwa:v0.7.17_cv1"
+    //container "https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7"
+
+    conda (params.conda ? "bioconda::bwa=0.7.17" : null)
+
+    input:
+    path fasta
+    val options
+
+    output:
+    path "${fasta}.*", emit: index
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    """
+    bwa index $ioptions.args $fasta
+    echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
+    """
+}

software/bwa/mem/functions.nf

@@ -0,0 +1 @@
+../../lib/functions.nf

software/bwa/mem/main.nf

@@ -0,0 +1,42 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process BWA_MEM {
+    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/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0"
+    //container "https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0"
+
+    conda (params.conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.10" : null)
+
+    input:
+    tuple val(meta), path(reads)
+    path index
+    path fasta
+    val options
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    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 rg       = meta.read_group ? "-R ${meta.read_group}" : ""
+    """
+    bwa mem \\
+        $ioptions.args \\
+        $rg \\
+        -t $task.cpus \\
+        $fasta \\
+        $reads \\
+        | samtools view $ioptions.args2 -@ $task.cpus -bS -o ${prefix}.bam -
+
+    echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
+    """
+}

software/deeptools/computematrix/functions.nf

@@ -0,0 +1 @@
+../../lib/functions.nf

software/deeptools/computematrix/main.nf

@@ -0,0 +1,41 @@
+// 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

@@ -0,0 +1 @@
+../../lib/functions.nf

software/deeptools/plotfingerprint/main.nf

@@ -0,0 +1,43 @@
+// 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

@@ -0,0 +1 @@
+../../lib/functions.nf

software/deeptools/plotheatmap/main.nf

@@ -0,0 +1,38 @@
+// 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

@@ -0,0 +1 @@
+../../lib/functions.nf

software/deeptools/plotprofile/main.nf

@@ -0,0 +1,38 @@
+// 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
+    """
+}

software/fastqc/functions.nf

@@ -0,0 +1 @@
+../lib/functions.nf

software/fastqc/lib

@@ -1 +0,0 @@
-../lib/

software/fastqc/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './lib/functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 process FASTQC {
     tag "$meta.id"

software/homer/annotatepeaks/functions.nf

@@ -0,0 +1 @@
+../../lib/functions.nf

software/homer/annotatepeaks/main.nf

@@ -0,0 +1,43 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+def VERSION = '4.11'
+
+process HOMER_ANNOTATEPEAKS {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${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/homer:4.11--pl526h9a982cc_2"
+    //container "https://depot.galaxyproject.org/singularity/homer:4.11--pl526h9a982cc_2"
+
+    conda (params.conda ? "bioconda::homer=4.11" : null)
+
+    input:
+    tuple val(meta), path(peak)
+    path fasta
+    path gtf
+    val options
+
+    output:
+    tuple val(meta), path("*annotatePeaks.txt"), emit: txt
+    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}"
+    """
+    annotatePeaks.pl \\
+        $peak \\
+        $fasta \\
+        $ioptions.args \\
+        -gtf $gtf \\
+        -cpu $task.cpus \\
+        > ${prefix}.annotatePeaks.txt
+
+    echo $VERSION > ${software}.version.txt
+    """
+}

software/macs2/callpeak/functions.nf

@@ -0,0 +1 @@
+../../lib/functions.nf

software/macs2/callpeak/main.nf

@@ -0,0 +1,47 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process MACS2_CALLPEAK {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${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/macs2:2.2.7.1--py37h516909a_0"
+    //container "https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py37h516909a_0"
+
+    conda (params.conda ? "bioconda::macs2=2.2.7.1" : null)
+
+    input:
+    tuple val(meta), path(ipbam), path(controlbam)
+    val macs2_gsize
+    val options
+
+    output:
+    tuple val(meta), path("*.{narrowPeak,broadPeak}"), emit: peak
+    tuple val(meta), path("*.xls"), emit: xls
+    tuple val(meta), path("*.gappedPeak"), emit: gapped optional true
+    tuple val(meta), path("*.bed"), emit: bed optional true
+    tuple val(meta), path("*.bdg"), emit: bdg optional true
+    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 format   = meta.single_end ? 'BAM' : 'BAMPE'
+    def control  = controlbam ? "--control $controlbam" : ''
+    """
+    macs2 \\
+        callpeak \\
+        $ioptions.args \\
+        --gsize $macs2_gsize \\
+        --format $format \\
+        --name $prefix \\
+        --treatment $ipbam \\
+         $control
+
+    macs2 --version | sed -e "s/macs2 //g" > ${software}.version.txt
+    """
+}

software/phantompeakqualtools/functions.nf

@@ -0,0 +1 @@
+../lib/functions.nf

software/phantompeakqualtools/main.nf

@@ -0,0 +1,37 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+def VERSION = '1.2.2'
+
+process PHANTOMPEAKQUALTOOLS {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${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/phantompeakqualtools:1.2.2--0"
+    //container "https://depot.galaxyproject.org/singularity/phantompeakqualtools:1.2.2--0"
+
+    conda (params.conda ? "bioconda::phantompeakqualtools=1.2.2" : null)
+
+    input:
+    tuple val(meta), path(bam)
+    val options
+
+    output:
+    tuple val(meta), path("*.out"), emit: spp
+    tuple val(meta), path("*.pdf"), emit: pdf
+    tuple val(meta), path("*.Rdata"), emit: rdata
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    """
+    RUN_SPP=`which run_spp.R`
+    Rscript -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" -p=$task.cpus
+    echo $VERSION > ${software}.version.txt
+    """
+}

software/picard/collectmultiplemetrics/functions.nf

@@ -0,0 +1 @@
+../../lib/functions.nf

software/picard/collectmultiplemetrics/main.nf

@@ -0,0 +1,47 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process PICARD_COLLECTMULTIPLEMETRICS {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${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/picard:2.23.2--0"
+    //container "https://depot.galaxyproject.org/singularity/picard:2.23.2--0"
+
+    conda (params.conda ? "bioconda::picard=2.23.2" : null)
+
+    input:
+    tuple val(meta), path(bam)
+    path fasta
+    val options
+
+    output:
+    tuple val(meta), path("*_metrics"), emit: metrics
+    tuple val(meta), path("*.pdf"), emit: pdf
+    path "*.version.txt", emit: version
+
+    script:
+    def software  = getSoftwareName(task.process)
+    def ioptions  = initOptions(options)
+    def prefix    = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+    """
+    picard \\
+        -Xmx${avail_mem}g \\
+        CollectMultipleMetrics \\
+        $ioptions.args \\
+        INPUT=$bam \\
+        OUTPUT=${prefix}.CollectMultipleMetrics \\
+        REFERENCE_SEQUENCE=$fasta
+
+    echo \$(picard CollectMultipleMetrics --version 2>&1) | awk -F' ' '{print \$NF}' > ${software}.version.txt
+    """
+}

software/picard/markduplicates/functions.nf

@@ -0,0 +1 @@
+../../lib/functions.nf

software/picard/markduplicates/main.nf

@@ -0,0 +1,46 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process PICARD_MARKDUPLICATES {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${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/picard:2.23.2--0"
+    //container "https://depot.galaxyproject.org/singularity/picard:2.23.2--0"
+
+    conda (params.conda ? "bioconda::picard=2.23.2" : null)
+
+    input:
+    tuple val(meta), path(bam)
+    val options
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    tuple val(meta), path("*.metrics.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}" : "${meta.id}"
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+    """
+    picard \\
+        -Xmx${avail_mem}g \\
+        MarkDuplicates \\
+        $ioptions.args \\
+        INPUT=$bam \\
+        OUTPUT=${prefix}.bam \\
+        METRICS_FILE=${prefix}.MarkDuplicates.metrics.txt
+
+    echo \$(picard MarkDuplicates --version 2>&1) | awk -F' ' '{print \$NF}' > ${software}.version.txt
+    """
+}

software/picard/mergesamfiles/functions.nf

@@ -0,0 +1 @@
+../../lib/functions.nf

software/picard/mergesamfiles/main.nf

@@ -0,0 +1,51 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process PICARD_MERGESAMFILES {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${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/picard:2.23.2--0"
+    //container "https://depot.galaxyproject.org/singularity/picard:2.23.2--0"
+
+    conda (params.conda ? "bioconda::picard=2.23.2" : null)
+
+    input:
+    tuple val(meta), path(bams)
+    val options
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    path "*.version.txt", emit: version
+
+    script:
+    def software  = getSoftwareName(task.process)
+    def ioptions  = initOptions(options)
+    def prefix    = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    def bam_files = bams.sort()
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[Picard MergeSamFiles] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+    if (bam_files.size() > 1) {
+        """
+        picard \\
+            -Xmx${avail_mem}g \\
+            MergeSamFiles \\
+            $ioptions.args \\
+            ${'INPUT='+bam_files.join(' INPUT=')} \\
+            OUTPUT=${prefix}.bam
+        echo \$(picard MergeSamFiles --version 2>&1) | awk -F' ' '{print \$NF}' > ${software}.version.txt
+        """
+    } else {
+        """
+        ln -s ${bam_files[0]} ${prefix}.bam
+        echo \$(picard MergeSamFiles --version 2>&1) | awk -F' ' '{print \$NF}' > ${software}.version.txt
+        """
+    }
+}

software/preseq/lcextrap/functions.nf

@@ -0,0 +1 @@
+../../lib/functions.nf

software/preseq/lcextrap/main.nf

@@ -0,0 +1,42 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process PRESEQ_LCEXTRAP {
+    tag "$meta.id"
+    label 'process_medium'
+    label 'error_ignore'
+    publishDir "${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/preseq:2.0.3--hf53bd2b_3"
+    //container "https://depot.galaxyproject.org/singularity/preseq:2.0.3--hf53bd2b_3"
+
+    conda (params.conda ? "bioconda::preseq=2.0.3" : null)
+
+    input:
+    tuple val(meta), path(bam)
+    val options
+
+    output:
+    tuple val(meta), path("*.ccurve.txt"), emit: ccurve
+    tuple val(meta), path("*.log"), emit: log
+    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 pe       = meta.single_end ? '' : '-pe'
+    """
+    preseq \\
+        lc_extrap \\
+        $ioptions.args \\
+        $pe \\
+        -output ${prefix}.ccurve.txt \\
+        $bam
+    cp .command.err ${prefix}.command.log
+
+    echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//' > ${software}.version.txt
+    """
+}

software/samtools/flagstat/functions.nf

@@ -0,0 +1 @@
+../../lib/functions.nf

software/samtools/flagstat/main.nf

@@ -0,0 +1,29 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process SAMTOOLS_FLAGSTAT {
+    tag "$meta.id"
+    publishDir "${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/samtools:1.10--h9402c20_2"
+    //container " https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+
+    conda (params.conda ? "bioconda::samtools=1.10" : null)
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+    val options
+
+    output:
+    tuple val(meta), path("*.flagstat"), emit: flagstat
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    """
+    samtools flagstat $bam > ${bam}.flagstat
+    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
+    """
+}

software/samtools/idxstats/functions.nf

@@ -0,0 +1 @@
+../../lib/functions.nf

software/samtools/idxstats/main.nf

@@ -0,0 +1,29 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process SAMTOOLS_IDXSTATS {
+    tag "$meta.id"
+    publishDir "${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/samtools:1.10--h9402c20_2"
+    //container " https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+
+    conda (params.conda ? "bioconda::samtools=1.10" : null)
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+    val options
+
+    output:
+    tuple val(meta), path("*.idxstats"), emit: idxstats
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    """
+    samtools idxstats $bam > ${bam}.idxstats
+    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
+    """
+}

software/samtools/index/functions.nf

@@ -0,0 +1 @@
+../../lib/functions.nf

software/samtools/index/main.nf

@@ -0,0 +1,29 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process SAMTOOLS_INDEX {
+    tag "$meta.id"
+    publishDir "${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/samtools:1.10--h9402c20_2"
+    //container " https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+
+    conda (params.conda ? "bioconda::samtools=1.10" : null)
+
+    input:
+    tuple val(meta), path(bam)
+    val options
+
+    output:
+    tuple val(meta), path("*.bai"), emit: bai
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    """
+    samtools index $bam
+    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
+    """
+}

software/samtools/sort/functions.nf

@@ -0,0 +1 @@
+../../lib/functions.nf

software/samtools/sort/main.nf

@@ -0,0 +1,32 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process SAMTOOLS_SORT {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${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/samtools:1.10--h9402c20_2"
+    //container " https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+
+    conda (params.conda ? "bioconda::samtools=1.10" : null)
+
+    input:
+    tuple val(meta), path(bam)
+    val options
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    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}"
+    """
+    samtools sort $ioptions.args -@ $task.cpus -o ${prefix}.bam -T $prefix $bam
+    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
+    """
+}

software/samtools/stats/functions.nf

@@ -0,0 +1 @@
+../../lib/functions.nf

software/samtools/stats/main.nf

@@ -0,0 +1,29 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process SAMTOOLS_STATS {
+    tag "$meta.id"
+    publishDir "${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/samtools:1.10--h9402c20_2"
+    //container " https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+
+    conda (params.conda ? "bioconda::samtools=1.10" : null)
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+    val options
+
+    output:
+    tuple val(meta), path("*.stats"), emit: stats
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    """
+    samtools stats $bam > ${bam}.stats
+    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
+    """
+}

software/subread/featurecounts/functions.nf

@@ -0,0 +1 @@
+../../lib/functions.nf

software/subread/featurecounts/main.nf

@@ -0,0 +1,41 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process SUBREAD_FEATURECOUNTS {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${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/subread:2.0.1--hed695b0_0"
+    //container "https://depot.galaxyproject.org/singularity/subread:2.0.1--hed695b0_0"
+
+    conda (params.conda ? "bioconda::subread=2.0.1" : null)
+
+    input:
+    tuple val(meta), path(bams), path(annotation)
+    val options
+
+    output:
+    tuple val(meta), path("*featureCounts.txt"), emit: txt
+    tuple val(meta), path("*featureCounts.txt.summary"), emit: summary
+    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 pe       = meta.single_end ? '' : '-p'
+    """
+    featureCounts \\
+        $ioptions.args \\
+        $pe \\
+        -T $task.cpus \\
+        -a $annotation \\
+        -o ${prefix}.featureCounts.txt \\
+        ${bams.join(' ')}
+
+    echo \$(featureCounts -v 2>&1) | sed -e "s/featureCounts v//g" > ${software}.version.txt
+    """
+}

software/trimgalore/functions.nf

@@ -0,0 +1 @@
+../lib/functions.nf

software/trimgalore/main.nf

@@ -0,0 +1,79 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process TRIMGALORE {
+    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/trim-galore:0.6.5--0"
+    //container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.5--0"
+
+    conda (params.conda ? "bioconda::trim-galore=0.6.5" : null)
+
+    input:
+    tuple val(meta), path(reads)
+    val options
+
+    output:
+    tuple val(meta), path("*.fq.gz"), emit: reads
+    tuple val(meta), path("*.html"), emit: html optional true
+    tuple val(meta), path("*.zip"), emit: zip optional true
+    tuple val(meta), path("*report.txt"), emit: log
+    path "*.version.txt", emit: version
+
+    script:
+    // Calculate number of --cores for TrimGalore based on value of task.cpus
+    // See: https://github.com/FelixKrueger/TrimGalore/blob/master/Changelog.md#version-060-release-on-1-mar-2019
+    // See: https://github.com/nf-core/atacseq/pull/65
+    def cores = 1
+    if (task.cpus) {
+        cores = (task.cpus as int) - 4
+        if (meta.single_end) cores = (task.cpus as int) - 3
+        if (cores < 1) cores = 1
+        if (cores > 4) cores = 4
+    }
+
+    // Clipping presets have to be evaluated in the context of SE/PE
+    def c_r1 = params.clip_r1 > 0 ? "--clip_r1 ${params.clip_r1}" : ''
+    def c_r2 = params.clip_r2 > 0 ? "--clip_r2 ${params.clip_r2}" : ''
+    def tpc_r1 = params.three_prime_clip_r1 > 0 ? "--three_prime_clip_r1 ${params.three_prime_clip_r1}" : ''
+    def tpc_r2 = params.three_prime_clip_r2 > 0 ? "--three_prime_clip_r2 ${params.three_prime_clip_r2}" : ''
+
+    // Added soft-links to original fastqs for consistent naming in MultiQC
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    if (meta.single_end) {
+        """
+        [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
+        trim_galore \\
+            $ioptions.args \\
+            --cores $cores \\
+            --gzip \\
+            $c_r1 \\
+            $tpc_r1 \\
+            ${prefix}.fastq.gz
+        echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//' > ${software}.version.txt
+        """
+    } else {
+        """
+        [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
+        [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
+        trim_galore \\
+            $ioptions.args \\
+            --cores $cores \\
+            --paired \\
+            --gzip \\
+            $c_r1 \\
+            $c_r2 \\
+            $tpc_r1 \\
+            $tpc_r2 \\
+            ${prefix}_1.fastq.gz \\
+            ${prefix}_2.fastq.gz
+        echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//' > ${software}.version.txt
+        """
+    }
+}

software/ucsc/bedgraphtobigwig/functions.nf

@@ -0,0 +1 @@
+../../lib/functions.nf

software/ucsc/bedgraphtobigwig/main.nf

@@ -0,0 +1,35 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+def VERSION = '377'
+
+process UCSC_BEDRAPHTOBIGWIG {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${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/ucsc-bedgraphtobigwig:377--h446ed27_1"
+    //container "https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:377--h446ed27_1"
+
+    conda (params.conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null)
+
+    input:
+    tuple val(meta), path(bedgraph)
+    path sizes
+    val options
+
+    output:
+    tuple val(meta), path("*.bigWig"), emit: bigwig
+    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}"
+    """
+    bedGraphToBigWig $bedgraph $sizes ${prefix}.bigWig
+    echo $VERSION > ${software}.version.txt
+    """
+}