Update tools not in rnaseq pipeline too

git_update.sh

@@ -0,0 +1,4 @@
+
+git pull
+git pull upstream master
+git push

software/SOFTWARE/TOOL/main.nf

@@ -10,7 +10,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
 // TODO nf-core: The key words "MUST", "MUST NOT", "SHOULD", etc. are to be interpreted as described in RFC 2119 (https://tools.ietf.org/html/rfc2119).
 // TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
 //               All other parameters MUST be provided as a string i.e. "options.args"
-//               where "options" is a Groovy Map that MUST be provided in the "input:" section of the process.
+//               where "params.options" is a Groovy Map that MUST be provided via the addParams section of the including workflow.
 //               Any parameters that need to be evaluated in the context of a particular sample
 //               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
 // TODO nf-core: Software that can be piped together SHOULD be added to separate module files
@@ -18,6 +18,9 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
 //               e.g. bwa mem | samtools view -B -T ref.fasta to output BAM instead of SAM.
 // TODO nf-core: Optional inputs are not currently supported by Nextflow. However, "fake files" MAY be used to work around this issue.
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 // TODO nf-core: Process name MUST be all uppercase,
 //               "SOFTWARE" and (ideally) "TOOL" MUST be all one word separated by an "_".
 process SOFTWARE_TOOL {
@@ -31,18 +34,22 @@ process SOFTWARE_TOOL {
         mode: params.publish_dir_mode,
         // TODO nf-core: If a meta map of sample information is NOT provided in "input:" section
         //               change "publish_id:meta.id" to initialise an empty string e.g. "publish_id:''".
-        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    // TODO nf-core: List required Conda packages.
+    //               Software MUST be pinned to channel (i.e. "bioconda") and version (i.e. "1.10") as in the example below.
+    //               Pinning the build too e.g. "bioconda::samtools=1.10=h9402c20_2" is not currently a requirement.
+    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
 
     // TODO nf-core: Fetch "docker pull" address for latest BioContainer image of software: e.g. https://biocontainers.pro/#/tools/samtools
     //               Click on the Pacakages and Containers tab, sort by Version and get the portion of the link after the docker pull command where Type is Docker.
     //               You may need to double-check that you are using the latest version of the software because you may find that containers for older versions have been rebuilt more recently.
     //               If required, multi-tool containers may also be available and are usually named to start with "mulled".
-    container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
-
+        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
-    // TODO nf-core: List required Conda packages.
+    } else {
-    //               Software MUST be pinned to channel (i.e. "bioconda") and version (i.e. "1.10") as in the example below.
+        container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
-    //               Pinning the build too e.g. "bioconda::samtools=1.10=h9402c20_2" is not currently a requirement.
+    }
-    conda (params.conda ? "bioconda::samtools=1.10" : null)
 
     input:
     // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
@@ -52,9 +59,7 @@ process SOFTWARE_TOOL {
     // TODO nf-core: Where applicable please provide/convert compressed files as input/output
     //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
     tuple val(meta), path(reads)
-    // TODO nf-core: List additional required input channels/values here
+    
-    val   options
-
     output:
     // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
     // TODO nf-core: If meta is provided in "input:" section then it MUST be added to ALL output channels (except version)
@@ -64,19 +69,18 @@ process SOFTWARE_TOOL {
 
     script:
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
     // TODO nf-core: If a meta map of sample information is NOT provided in "input:" section delete the line below
-    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
     //               If the software is unable to output a version number on the command-line then it can be manually specified
     //               e.g. https://github.com/nf-core/modules/blob/master/software/homer/annotatepeaks/main.nf
-    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$ioptions.args" variable
+    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$options.args" variable
     // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
     //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
     // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
     """
     software tool \\
-        $ioptions.args \\
+        $options.args \\
         --threads $task.cpus \\
         $reads \\
         > ${prefix}.bam

software/bwa/index/main.nf

@@ -1,31 +1,34 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
-    container "biocontainers/bwa:v0.7.17_cv1"
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null)
-    //container "https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7"
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
-
+        container "https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7"
-    conda (params.conda ? "bioconda::bwa=0.7.17" : null)
+    } else {
+        container "biocontainers/bwa:v0.7.17_cv1"
+    }
 
     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
+    bwa index $options.args $fasta
     echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
     """
 }

software/bwa/mem/main.nf

@@ -1,41 +1,44 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    container "quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0"
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.10" : null)
-    //container "https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0"
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
-
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0"
-    conda (params.conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.10" : null)
+    } else {
+        container "quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0"
+    }
 
     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     = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix     = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
     """
     bwa mem \\
-        $ioptions.args \\
+        $options.args \\
         $read_group \\
         -t $task.cpus \\
         $fasta \\
         $reads \\
-        | samtools view $ioptions.args2 -@ $task.cpus -bS -o ${prefix}.bam -
+        | samtools view $options.args2 -@ $task.cpus -bS -o ${prefix}.bam -
 
     echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
     """

software/deeptools/computematrix/main.nf

@@ -1,23 +1,27 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    container "quay.io/biocontainers/deeptools:3.4.3--py_0"
+    conda (params.enable_conda ? "bioconda::deeptools=3.4.3" : null)
-    //container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0"
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
-
+        container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0"
-    conda (params.conda ? "bioconda::deeptools=3.4.3" : null)
+    } else {
+        container "quay.io/biocontainers/deeptools:3.4.3--py_0"
+    }
 
     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
@@ -25,11 +29,10 @@ process DEEPTOOLS_COMPUTEMATRIX {
 
     script:
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     """
     computeMatrix \\
-        $ioptions.args \\
+        $options.args \\
         --regionsFileName $bed \\
         --scoreFileName $bigwig \\
         --outFileName ${prefix}.computeMatrix.mat.gz \\

software/deeptools/plotfingerprint/main.nf

@@ -1,22 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    container "quay.io/biocontainers/deeptools:3.4.3--py_0"
+    conda (params.enable_conda ? "bioconda::deeptools=3.4.3" : null)
-    //container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0"
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
-
+        container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0"
-    conda (params.conda ? "bioconda::deeptools=3.4.3" : null)
+    } else {
+        container "quay.io/biocontainers/deeptools:3.4.3--py_0"
+    }
 
     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
@@ -25,12 +29,11 @@ process DEEPTOOLS_PLOTFINGERPRINT {
 
     script:
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     def extend   = (meta.single_end && params.fragment_size > 0) ? "--extendReads ${params.fragment_size}" : ''
     """
     plotFingerprint \\
-        $ioptions.args \\
+        $options.args \\
         $extend \\
         --bamfiles ${bams.join(' ')} \\
         --plotFile ${prefix}.plotFingerprint.pdf \\

software/deeptools/plotheatmap/main.nf

@@ -1,22 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    container "quay.io/biocontainers/deeptools:3.4.3--py_0"
+    conda (params.enable_conda ? "bioconda::deeptools=3.4.3" : null)
-    //container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0"
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
-
+        container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0"
-    conda (params.conda ? "bioconda::deeptools=3.4.3" : null)
+    } else {
+        container "quay.io/biocontainers/deeptools:3.4.3--py_0"
+    }
 
     input:
     tuple val(meta), path(matrix)
-    val   options
+    
-
     output:
     tuple val(meta), path("*.pdf"), emit: pdf
     tuple val(meta), path("*.tab"), emit: table
@@ -24,11 +28,10 @@ process DEEPTOOLS_PLOTHEATMAP {
 
     script:
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     """
     plotHeatmap \\
-        $ioptions.args \\
+        $options.args \\
         --matrixFile $matrix \\
         --outFileName ${prefix}.plotHeatmap.pdf \\
         --outFileNameMatrix ${prefix}.plotHeatmap.mat.tab

software/deeptools/plotprofile/main.nf

@@ -1,22 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    container "quay.io/biocontainers/deeptools:3.4.3--py_0"
+    conda (params.enable_conda ? "bioconda::deeptools=3.4.3" : null)
-    //container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0"
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
-
+        container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0"
-    conda (params.conda ? "bioconda::deeptools=3.4.3" : null)
+    } else {
+        container "quay.io/biocontainers/deeptools:3.4.3--py_0"
+    }
 
     input:
     tuple val(meta), path(matrix)
-    val   options
+    
-
     output:
     tuple val(meta), path("*.pdf"), emit: pdf
     tuple val(meta), path("*.tab"), emit: table
@@ -24,11 +28,10 @@ process DEEPTOOLS_PLOTPROFILE {
 
     script:
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     """
     plotProfile \\
-        $ioptions.args \\
+        $options.args \\
         --matrixFile $matrix \\
         --outFileName ${prefix}.plotProfile.pdf \\
         --outFileNameData ${prefix}.plotProfile.tab

software/homer/annotatepeaks/main.nf

@@ -1,6 +1,9 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 def VERSION = '4.11'
 
 process HOMER_ANNOTATEPEAKS {
@@ -8,18 +11,19 @@ process HOMER_ANNOTATEPEAKS {
     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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    container "quay.io/biocontainers/homer:4.11--pl526h9a982cc_2"
+    conda (params.enable_conda ? "bioconda::homer=4.11" : null)
-    //container "https://depot.galaxyproject.org/singularity/homer:4.11--pl526h9a982cc_2"
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
-
+        container "https://depot.galaxyproject.org/singularity/homer:4.11--pl526h9a982cc_2"
-    conda (params.conda ? "bioconda::homer=4.11" : null)
+    } else {
+        container "quay.io/biocontainers/homer:4.11--pl526h9a982cc_2"
+    }
 
     input:
     tuple val(meta), path(peak)
     path  fasta
     path  gtf
-    val   options
 
     output:
     tuple val(meta), path("*annotatePeaks.txt"), emit: txt
@@ -27,13 +31,12 @@ process HOMER_ANNOTATEPEAKS {
 
     script:
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     """
     annotatePeaks.pl \\
         $peak \\
         $fasta \\
-        $ioptions.args \\
+        $options.args \\
         -gtf $gtf \\
         -cpu $task.cpus \\
         > ${prefix}.annotatePeaks.txt

software/macs2/callpeak/main.nf

@@ -1,23 +1,27 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    container "quay.io/biocontainers/macs2:2.2.7.1--py37h516909a_0"
+    conda (params.enable_conda ? "bioconda::macs2=2.2.7.1" : null)
-    //container "https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py37h516909a_0"
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
-
+        container "https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py37h516909a_0"
-    conda (params.conda ? "bioconda::macs2=2.2.7.1" : null)
+    } else {
+        container "quay.io/biocontainers/macs2:2.2.7.1--py37h516909a_0"
+    }
 
     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
@@ -29,14 +33,13 @@ process MACS2_CALLPEAK {
 
     script:
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     def format   = meta.single_end ? 'BAM' : 'BAMPE'
     def control  = controlbam ? "--control $controlbam" : ''
     """
     macs2 \\
         callpeak \\
-        $ioptions.args \\
+        $options.args \\
         --gsize $macs2_gsize \\
         --format $format \\
         --name $prefix \\

software/phantompeakqualtools/main.nf

@@ -1,6 +1,9 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 def VERSION = '1.2.2'
 
 process PHANTOMPEAKQUALTOOLS {
@@ -8,17 +11,18 @@ process PHANTOMPEAKQUALTOOLS {
     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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    container "quay.io/biocontainers/phantompeakqualtools:1.2.2--0"
+    conda (params.enable_conda ? "bioconda::phantompeakqualtools=1.2.2" : null)
-    //container "https://depot.galaxyproject.org/singularity/phantompeakqualtools:1.2.2--0"
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
-
+        container "https://depot.galaxyproject.org/singularity/phantompeakqualtools:1.2.2--0"
-    conda (params.conda ? "bioconda::phantompeakqualtools=1.2.2" : null)
+    } else {
+        container "quay.io/biocontainers/phantompeakqualtools:1.2.2--0"
+    }
 
     input:
     tuple val(meta), path(bam)
-    val   options
+    
-
     output:
     tuple val(meta), path("*.out")  , emit: spp
     tuple val(meta), path("*.pdf")  , emit: pdf
@@ -27,8 +31,7 @@ process PHANTOMPEAKQUALTOOLS {
 
     script:
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix   = ioptions.suffix ? "${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

software/picard/collectmultiplemetrics/main.nf

@@ -1,22 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    container "quay.io/biocontainers/picard:2.23.6--0"
+    conda (params.enable_conda ? "bioconda::picard=2.23.6" : null)
-    //container "https://depot.galaxyproject.org/singularity/picard:2.23.6--0"
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
-
+        container "https://depot.galaxyproject.org/singularity/picard:2.23.6--0"
-    conda (params.conda ? "bioconda::picard=2.23.6" : null)
+    } else {
+        container "quay.io/biocontainers/picard:2.23.6--0"
+    }
 
     input:
     tuple val(meta), path(bam)
     path  fasta
-    val   options
 
     output:
     tuple val(meta), path("*_metrics"), emit: metrics
@@ -25,8 +29,7 @@ process PICARD_COLLECTMULTIPLEMETRICS {
 
     script:
     def software  = getSoftwareName(task.process)
-    def ioptions  = initOptions(options)
+    def prefix    = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix    = ioptions.suffix ? "${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.'
@@ -37,7 +40,7 @@ process PICARD_COLLECTMULTIPLEMETRICS {
     picard \\
         -Xmx${avail_mem}g \\
         CollectMultipleMetrics \\
-        $ioptions.args \\
+        $options.args \\
         INPUT=$bam \\
         OUTPUT=${prefix}.CollectMultipleMetrics \\
         REFERENCE_SEQUENCE=$fasta

software/picard/markduplicates/main.nf

@@ -1,22 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    container "quay.io/biocontainers/picard:2.23.6--0"
+    conda (params.enable_conda ? "bioconda::picard=2.23.6" : null)
-    //container "https://depot.galaxyproject.org/singularity/picard:2.23.6--0"
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
-
+        container "https://depot.galaxyproject.org/singularity/picard:2.23.6--0"
-    conda (params.conda ? "bioconda::picard=2.23.6" : null)
+    } else {
+        container "quay.io/biocontainers/picard:2.23.6--0"
+    }
 
     input:
     tuple val(meta), path(bam)
-    val   options
+    
-
     output:
     tuple val(meta), path("*.bam")        , emit: bam
     tuple val(meta), path("*.metrics.txt"), emit: metrics
@@ -24,8 +28,7 @@ process PICARD_MARKDUPLICATES {
 
     script:
     def software  = getSoftwareName(task.process)
-    def ioptions  = initOptions(options)
+    def prefix    = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix    = ioptions.suffix ? "${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.'
@@ -36,7 +39,7 @@ process PICARD_MARKDUPLICATES {
     picard \\
         -Xmx${avail_mem}g \\
         MarkDuplicates \\
-        $ioptions.args \\
+        $options.args \\
         INPUT=$bam \\
         OUTPUT=${prefix}.bam \\
         METRICS_FILE=${prefix}.MarkDuplicates.metrics.txt

software/picard/mergesamfiles/main.nf

@@ -1,30 +1,33 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    container "quay.io/biocontainers/picard:2.23.6--0"
+    conda (params.enable_conda ? "bioconda::picard=2.23.6" : null)
-    //container "https://depot.galaxyproject.org/singularity/picard:2.23.6--0"
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
-
+        container "https://depot.galaxyproject.org/singularity/picard:2.23.6--0"
-    conda (params.conda ? "bioconda::picard=2.23.6" : null)
+    } else {
+        container "quay.io/biocontainers/picard:2.23.6--0"
+    }
 
     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    = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix    = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     def bam_files = bams.sort()
     def avail_mem = 3
     if (!task.memory) {
@@ -37,7 +40,7 @@ process PICARD_MERGESAMFILES {
         picard \\
             -Xmx${avail_mem}g \\
             MergeSamFiles \\
-            $ioptions.args \\
+            $options.args \\
             ${'INPUT='+bam_files.join(' INPUT=')} \\
             OUTPUT=${prefix}.bam
         echo \$(picard MergeSamFiles --version 2>&1) | awk -F' ' '{print \$NF}' > ${software}.version.txt

software/ucsc/bedgraphtobigwig/main.nf

@@ -1,6 +1,9 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 def VERSION = '377'
 
 process UCSC_BEDRAPHTOBIGWIG {
@@ -8,26 +11,26 @@ process UCSC_BEDRAPHTOBIGWIG {
     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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    container "quay.io/biocontainers/ucsc-bedgraphtobigwig:377--h446ed27_1"
+    conda (params.enable_conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null)
-    //container "https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:377--h446ed27_1"
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
-
+        container "https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:377--h446ed27_1"
-    conda (params.conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null)
+    } else {
+        container "quay.io/biocontainers/ucsc-bedgraphtobigwig:377--h446ed27_1"
+    }
 
     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   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     """
     bedGraphToBigWig $bedgraph $sizes ${prefix}.bigWig
     echo $VERSION > ${software}.version.txt