Merge pull request #70 from drpatelh/versions

Update existing modules with new options and container syntax

README.md

@@ -80,7 +80,7 @@ We have written a helper command in the `nf-core/tools` package that uses the Gi
 
     nextflow.enable.dsl = 2
 
-    include { FASTQC } from './modules/nf-core/software/fastqc/main'
+    include { FASTQC } from './modules/nf-core/software/fastqc/main' addParams( options: [:] )
     ```
 
 5. We have plans to add other utility commands to help developers install and maintain modules downloaded from this repository so watch this space!
@@ -170,7 +170,7 @@ using a combination of `bwa` and `samtools` to output a BAM file instead of a SA
 
 - A module file SHOULD only define input and output files as command-line parameters to be executed within the process.
 
-- 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.
+- All other parameters MUST be provided as a string i.e. `options.args` where `options` is a Groovy Map that MUST be provided via the Nextflow `addParams` option when including the module via `include` in the parent workflow.
 
 - If the tool supports multi-threading then you MUST provide the appropriate parameter using the Nextflow `task` variable e.g. `--threads $task.cpus`.
 
@@ -207,7 +207,7 @@ The [Nextflow `publishDir`](https://www.nextflow.io/docs/latest/process.html#pub
 ```nextflow
     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) }
 ```
 
 The `saveFiles` function can be found in the [`functions.nf`](software/fastqc/functions.nf) file of utility functions that will be copied into all module directories. It uses the various publishing `options` specified as input to the module to construct and append the relevant output path to `params.outdir`.

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".
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+    } else {
         container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
-
+    }
-    // 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.conda ? "bioconda::samtools=1.10" : null)
 
     input:
     // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
@@ -52,8 +59,6 @@ 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
@@ -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/SOFTWARE/TOOL/meta.yml

@@ -32,7 +32,7 @@ params:
         description: |
             Value for the Nextflow `publishDir` mode parameter.
             Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - conda:
+    - enable_conda:
         type: boolean
         description: |
             Run the module with Conda using the software specified
@@ -49,11 +49,6 @@ input:
         description: |
             List of input FastQ files of size 1 and 2 for single-end and paired-end data,
             respectively.
-    - options:
-        type: map
-        description: |
-            Groovy Map containing module options for passing command-line arguments and
-            output file paths.
 ## TODO nf-core: Add a description of all of the variables used as output
 output:
     - meta:

software/SOFTWARE/TOOL/test/main.nf

@@ -2,7 +2,8 @@
 
 nextflow.enable.dsl = 2
 
-include { FASTQC } from '../main.nf'
+include { FASTQC as FASTQC_SE } from '../main.nf'  addParams( options: [ publish_dir:'test_single_end' ] )
+include { FASTQC as FASTQC_PE } from '../main.nf'  addParams( options: [ publish_dir:'test_paired_end' ] )
 
 /*
  * Test with single-end data
@@ -13,7 +14,7 @@ workflow test_single_end {
     input = [ [ id:'test', single_end:true ], // meta map
               [ file("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ]
 
-    FASTQC ( input, [ publish_dir:'test_single_end' ] )
+    FASTQC_SE ( input )
 }
 
 /*
@@ -26,7 +27,7 @@ workflow test_paired_end {
               [ file("${baseDir}/input/test_R1.fastq.gz", checkIfExists: true),
                 file("${baseDir}/input/test_R2.fastq.gz", checkIfExists: true) ] ]
 
-    FASTQC ( input, [ publish_dir:'test_paired_end' ] )
+    FASTQC_PE ( input )
 }
 
 workflow {

software/SOFTWARE/TOOL/test/nextflow.config

@@ -2,12 +2,12 @@
 params {
     outdir = "output/"
     publish_dir_mode = "copy"
-    conda = false
+    enable_conda = false
 }
 
 profiles {
     conda  {
-        params.conda = true
+        params.enable_conda = true
     }
     docker {
         docker.enabled = true

software/bwa/index/main.nf

@@ -1,21 +1,25 @@
 // 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:'') }
 
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7"
+    } else {
         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
@@ -23,9 +27,8 @@ process BWA_INDEX {
 
     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/index/meta.yml

@@ -24,7 +24,7 @@ params:
         description: |
             Value for the Nextflow `publishDir` mode parameter.
             Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - conda:
+    - enable_conda:
         type: boolean
         description: |
             Run the module with Conda using the software specified
@@ -33,11 +33,6 @@ input:
     - fasta:
         type: file
         description: Input genome fasta file
-    - options:
-        type: map
-        description: |
-            Groovy Map containing module options for passing command-line arguments and
-            output file paths.
 output:
     - index:
         type: file

software/bwa/index/test/main.nf

@@ -2,10 +2,10 @@
 
 nextflow.enable.dsl = 2
 
-include { BWA_INDEX } from '../main.nf'
+include { BWA_INDEX } from '../main.nf' addParams( options: [:] )
 
 workflow test {
-    BWA_INDEX ( file("${baseDir}/input/NC_010473.fa", checkIfExists: true), [:] )
+    BWA_INDEX ( file("${baseDir}/input/NC_010473.fa", checkIfExists: true) )
 }
 
 workflow {

software/bwa/index/test/nextflow.config

@@ -2,12 +2,12 @@
 params {
     outdir = "output/"
     publish_dir_mode = "copy"
-    conda = false
+    enable_conda = false
 }
 
 profiles {
     conda  {
-        params.conda = true
+        params.enable_conda = true
     }
     docker {
         docker.enabled = true

software/bwa/mem/main.nf

@@ -1,23 +1,27 @@
 // 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) }
 
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0"
+    } else {
         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
@@ -25,17 +29,16 @@ process BWA_MEM {
 
     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/bwa/mem/meta.yml

@@ -27,7 +27,7 @@ params:
         description: |
             Value for the Nextflow `publishDir` mode parameter.
             Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - conda:
+    - enable_conda:
         type: boolean
         description: |
             Run the module with Conda using the software specified
@@ -50,11 +50,6 @@ input:
     - fasta:
         type: file
         description: Input genome fasta file
-    - options:
-        type: map
-        description: |
-            Groovy Map containing module options for passing command-line arguments and
-            output file paths.
 output:
     - bam:
         type: file

software/bwa/mem/test/main.nf

@@ -2,7 +2,8 @@
 
 nextflow.enable.dsl = 2
 
-include { BWA_MEM } from '../main.nf'
+include { BWA_MEM as BWA_MEM_SE } from '../main.nf'  addParams( options: [ publish_dir:'test_single_end' ] )
+include { BWA_MEM as BWA_MEM_PE } from '../main.nf'  addParams( options: [ publish_dir:'test_paired_end' ] )
 
 /*
  * Test with single-end data
@@ -13,11 +14,10 @@ workflow test_single_end {
     input = [ [ id:'test', single_end:true ], // meta map
               [ file("${baseDir}/input/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ]
 
-    BWA_MEM (
+    BWA_MEM_SE (
         input,
         file("${baseDir}/input/index/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
-        file("${baseDir}/input/NC_010473.fa", checkIfExists: true),
+        file("${baseDir}/input/NC_010473.fa", checkIfExists: true)
-        [ publish_dir:'test_single_end' ]
     )
 }
 
@@ -31,11 +31,10 @@ workflow test_paired_end {
               [ file("${baseDir}/input/Ecoli_DNA_R1.fastq.gz", checkIfExists: true),
                 file("${baseDir}/input/Ecoli_DNA_R2.fastq.gz", checkIfExists: true) ] ]
 
-    BWA_MEM (
+    BWA_MEM_PE (
         input,
         file("${baseDir}/input/index/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
-        file("${baseDir}/input/NC_010473.fa", checkIfExists: true),
+        file("${baseDir}/input/NC_010473.fa", checkIfExists: true)
-        [ publish_dir:'test_paired_end' ]
     )
 }
 

software/bwa/mem/test/nextflow.config

@@ -2,12 +2,12 @@
 params {
     outdir = "output/"
     publish_dir_mode = "copy"
-    conda = false
+    enable_conda = false
 }
 
 profiles {
     conda  {
-        params.conda = true
+        params.enable_conda = true
     }
     docker {
         docker.enabled = true

software/deeptools/computematrix/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_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) }
 
+    conda (params.enable_conda ? "bioconda::deeptools=3.4.3" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0"
+    } else {
         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
@@ -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

@@ -1,21 +1,25 @@
 // 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) }
 
+    conda (params.enable_conda ? "bioconda::deeptools=3.4.3" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0"
+    } else {
         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
@@ -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

@@ -1,21 +1,25 @@
 // 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) }
 
+    conda (params.enable_conda ? "bioconda::deeptools=3.4.3" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0"
+    } else {
         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
@@ -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

@@ -1,21 +1,25 @@
 // 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) }
 
+    conda (params.enable_conda ? "bioconda::deeptools=3.4.3" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0"
+    } else {
         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
@@ -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/fastqc/main.nf

@@ -1,21 +1,25 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 process FASTQC {
     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) }
 
+    conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0"
+    } else {
         container "quay.io/biocontainers/fastqc:0.11.9--0"
-    //container "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0"
+    }
-
-    conda (params.conda ? "bioconda::fastqc=0.11.9" : null)
     
     input:
     tuple val(meta), path(reads)
-    val   options
     
     output:
     tuple val(meta), path("*.html"), emit: html
@@ -25,19 +29,18 @@ process FASTQC {
     script:
     // Add soft-links to original FastQs for consistent naming in pipeline
     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}"
     if (meta.single_end) {
         """
         [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
-        fastqc $ioptions.args --threads $task.cpus ${prefix}.fastq.gz
+        fastqc $options.args --threads $task.cpus ${prefix}.fastq.gz
         fastqc --version | sed -e "s/FastQC v//g" > ${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
-        fastqc $ioptions.args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
+        fastqc $options.args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
         fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt
         """
     }

software/fastqc/meta.yml

@@ -26,7 +26,7 @@ params:
         description: |
             Value for the Nextflow `publishDir` mode parameter.
             Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - conda:
+    - enable_conda:
         type: boolean
         description: |
             Run the module with Conda using the software specified
@@ -42,11 +42,6 @@ input:
         description: |
             List of input FastQ files of size 1 and 2 for single-end and paired-end data,
             respectively.
-    - options:
-        type: map
-        description: |
-            Groovy Map containing module options for passing command-line arguments and
-            output file paths.
 output:
     - meta:
         type: map

software/fastqc/test/main.nf

@@ -2,7 +2,8 @@
 
 nextflow.enable.dsl = 2
 
-include { FASTQC } from '../main.nf'
+include { FASTQC as FASTQC_SE } from '../main.nf'  addParams( options: [ publish_dir:'test_single_end' ] )
+include { FASTQC as FASTQC_PE } from '../main.nf'  addParams( options: [ publish_dir:'test_paired_end' ] )
 
 /*
  * Test with single-end data
@@ -13,7 +14,7 @@ workflow test_single_end {
     input = [ [ id:'test', single_end:true ], // meta map
               [ file("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ]
 
-    FASTQC ( input, [ publish_dir:'test_single_end' ] )
+    FASTQC_SE ( input )
 }
 
 /*
@@ -26,7 +27,7 @@ workflow test_paired_end {
               [ file("${baseDir}/input/test_R1.fastq.gz", checkIfExists: true),
                 file("${baseDir}/input/test_R2.fastq.gz", checkIfExists: true) ] ]
 
-    FASTQC ( input, [ publish_dir:'test_paired_end' ] )
+    FASTQC_PE ( input )
 }
 
 workflow {

software/fastqc/test/nextflow.config

@@ -2,12 +2,12 @@
 params {
     outdir = "output/"
     publish_dir_mode = "copy"
-    conda = false
+    enable_conda = false
 }
 
 profiles {
     conda  {
-        params.conda = true
+        params.enable_conda = true
     }
     docker {
         docker.enabled = true

software/gffread/main.nf

@@ -1,20 +1,24 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 process GFFREAD {
     tag "$gff"
     publishDir "${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:'') }
 
+    conda (params.enable_conda ? "bioconda::gffread=0.12.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0"
+    } else {
         container "quay.io/biocontainers/gffread:0.12.1--h8b12597_0"
-    //container https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0
+    }
-
-    conda (params.conda ? "bioconda::gffread=0.12.1" : null)
 
     input:
     path gff
-    val  options
     
     output:
     path "*.gtf"        , emit: gtf
@@ -22,9 +26,8 @@ process GFFREAD {
 
     script:
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
     """
-    gffread $gff $ioptions.args -o ${gff.baseName}.gtf
+    gffread $gff $options.args -o ${gff.baseName}.gtf
     echo \$(gffread --version 2>&1) > ${software}.version.txt
     """
 }

software/hisat2/align/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 = '2.2.0'
 
 process HISAT2_ALIGN {
@@ -8,18 +11,19 @@ process HISAT2_ALIGN {
     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) }
 
+    conda (params.enable_conda ? "bioconda::hisat2=2.2.0 bioconda::samtools=1.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0"
+    } else {
         container "quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0"
-    //container "https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0"
+    }
-
-    conda (params.conda ? "bioconda::hisat2=2.2.0 bioconda::samtools=1.10" : null)
 
     input:
     tuple val(meta), path(reads)
     path  index
     path  splicesites
-    val   options
     
     output:
     tuple val(meta), path("*.bam"), emit: bam
@@ -30,8 +34,7 @@ process HISAT2_ALIGN {
 
     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 strandedness = ''
     if (meta.strandedness == 'forward') {
@@ -53,7 +56,7 @@ process HISAT2_ALIGN {
             --threads $task.cpus \\
             $seq_center \\
             $unaligned \\
-            $ioptions.args \\
+            $options.args \\
             | samtools view -bS -F 4 -F 256 - > ${prefix}.bam
 
         echo $VERSION > ${software}.version.txt
@@ -74,7 +77,7 @@ process HISAT2_ALIGN {
             $unaligned \\
             --no-mixed \\
             --no-discordant \\
-            $ioptions.args \\
+            $options.args \\
             | samtools view -bS -F 4 -F 8 -F 256 - > ${prefix}.bam
 
         if [ -f ${prefix}.unmapped.fastq.1.gz ]; then

software/hisat2/build/main.nf

@@ -1,24 +1,28 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 def VERSION = '2.2.0'
 
 process HISAT2_BUILD {
     tag "$fasta"
     publishDir "${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:'') }
 
+    conda (params.enable_conda ? "bioconda::hisat2=2.2.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
+    } else {
         container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
-    //container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
+    }
-
-    conda (params.conda ? "bioconda::hisat2=2.2.0" : null)
 
     input:
     path fasta
     path gtf
     path splicesites
-    val  options
 
     output:
     path "hisat2",        emit: index
@@ -47,7 +51,6 @@ process HISAT2_BUILD {
     }
 
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
     """
     mkdir hisat2
     $extract_exons
@@ -55,7 +58,7 @@ process HISAT2_BUILD {
         -p $task.cpus \\
         $ss \\
         $exon \\
-        $ioptions.args \\
+        $options.args \\
         $fasta \\
         hisat2/${fasta.baseName}
 

software/hisat2/extractsplicesites/main.nf

@@ -1,22 +1,25 @@
 // Import generic module functions
 include { saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+
 def VERSION = '2.2.0'
 
 process HISAT2_EXTRACTSPLICESITES {
     tag "$gtf"
     publishDir "${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:'') }
 
+    conda (params.enable_conda ? "bioconda::hisat2=2.2.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
+    } else {
         container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
-    //container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
+    }
-
-    conda (params.conda ? "bioconda::hisat2=2.2.0" : null)
 
     input:
     path gtf
-    val  options
 
     output:
     path "*.splice_sites.txt", emit: txt

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) }
 
+    conda (params.enable_conda ? "bioconda::homer=4.11" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/homer:4.11--pl526h9a982cc_2"
+    } else {
         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
@@ -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

@@ -1,22 +1,26 @@
 // 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) }
 
+    conda (params.enable_conda ? "bioconda::macs2=2.2.7.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py37h516909a_0"
+    } else {
         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
@@ -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/macs2/functions.nf

@@ -1,59 +0,0 @@
-/*
- * -----------------------------------------------------
- *  Utility functions used in nf-core DSL2 module files
- * -----------------------------------------------------
- */
-
-/*
- * Extract name of software tool from process name using $task.process
- */
-def getSoftwareName(task_process) {
-    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-/*
- * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
- */
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args          = args.args ?: ''
-    options.args2         = args.args2 ?: ''
-    options.publish_by_id = args.publish_by_id ?: false
-    options.publish_dir   = args.publish_dir ?: ''
-    options.publish_files = args.publish_files
-    options.suffix        = args.suffix ?: ''
-    return options
-}
-
-/*
- * Tidy up and join elements of a list to return a path string
- */
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
-    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-/*
- * Function to save/publish module results
- */
-def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_id) {
-            path_list.add(args.publish_id)
-        }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
-            }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
-        }
-    }
-}

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 {
@@ -8,16 +11,17 @@ 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) }
 
+    conda (params.enable_conda ? "bioconda::phantompeakqualtools=1.2.2" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/phantompeakqualtools:1.2.2--0"
+    } else {
         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
@@ -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) }
 
+    conda (params.enable_conda ? "bioconda::picard=2.23.6" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/picard:2.23.6--0"
+    } else {
         container "quay.io/biocontainers/picard:2.23.6--0"
-    //container "https://depot.galaxyproject.org/singularity/picard:2.23.6--0"
+    }
-
-    conda (params.conda ? "bioconda::picard=2.23.6" : null)
 
     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/collectmultiplemetrics/meta.yml

@@ -25,7 +25,7 @@ params:
         description: |
             Value for the Nextflow `publishDir` mode parameter.
             Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - conda:
+    - enable_conda:
         type: boolean
         description: |
             Run the module with Conda using the software specified
@@ -43,11 +43,6 @@ input:
     - fasta:
         type: file
         description: Genome fasta file
-    - options:
-        type: map
-        description: |
-            Groovy Map containing module options for passing command-line arguments and
-            output file paths.
 output:
     - meta:
         type: map

software/picard/collectmultiplemetrics/test/main.nf

@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { PICARD_COLLECTMULTIPLEMETRICS } from '../main.nf'
+include { PICARD_COLLECTMULTIPLEMETRICS } from '../main.nf' addParams( options: [:] )
 
 workflow test {
 
@@ -12,8 +12,7 @@ workflow test {
 
     PICARD_COLLECTMULTIPLEMETRICS (
         input,
-        file("${baseDir}/input/NC_010473.fa", checkIfExists: true),
+        file("${baseDir}/input/NC_010473.fa", checkIfExists: true)
-        [:]
     )
 }
 

software/picard/collectmultiplemetrics/test/nextflow.config

@@ -2,12 +2,12 @@
 params {
     outdir = "output/"
     publish_dir_mode = "copy"
-    conda = false
+    enable_conda = false
 }
 
 profiles {
     conda  {
-        params.conda = true
+        params.enable_conda = true
     }
     docker {
         docker.enabled = true

software/picard/markduplicates/main.nf

@@ -1,21 +1,25 @@
 // 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) }
 
+    conda (params.enable_conda ? "bioconda::picard=2.23.6" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/picard:2.23.6--0"
+    } else {
         container "quay.io/biocontainers/picard:2.23.6--0"
-    //container "https://depot.galaxyproject.org/singularity/picard:2.23.6--0"
+    }
-
-    conda (params.conda ? "bioconda::picard=2.23.6" : null)
 
     input:
     tuple val(meta), path(bam)
-    val   options
     
     output:
     tuple val(meta), path("*.bam")        , emit: bam
@@ -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/markduplicates/meta.yml

@@ -25,7 +25,7 @@ params:
         description: |
             Value for the Nextflow `publishDir` mode parameter.
             Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - conda:
+    - enable_conda:
         type: boolean
         description: |
             Run the module with Conda using the software specified
@@ -40,11 +40,6 @@ input:
         type: file
         description: BAM file
         pattern: "*.{bam}"
-    - options:
-        type: map
-        description: |
-            Groovy Map containing module options for passing command-line arguments and
-            output file paths.
 output:
     - meta:
         type: map

software/picard/markduplicates/test/main.nf

@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { PICARD_MARKDUPLICATES } from '../main.nf'
+include { PICARD_MARKDUPLICATES } from '../main.nf' addParams( options: [:] )
 
 workflow test {
 
@@ -10,7 +10,7 @@ workflow test {
     input = [ [ id:'test', single_end:false ], // meta map
               file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true) ]
 
-    PICARD_MARKDUPLICATES ( input, [:] )
+    PICARD_MARKDUPLICATES ( input )
 }
 
 workflow {

software/picard/markduplicates/test/nextflow.config

@@ -2,12 +2,12 @@
 params {
     outdir = "output/"
     publish_dir_mode = "copy"
-    conda = false
+    enable_conda = false
 }
 
 profiles {
     conda  {
-        params.conda = true
+        params.enable_conda = true
     }
     docker {
         docker.enabled = true

software/picard/mergesamfiles/main.nf

@@ -1,21 +1,25 @@
 // 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) }
 
+    conda (params.enable_conda ? "bioconda::picard=2.23.6" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/picard:2.23.6--0"
+    } else {
         container "quay.io/biocontainers/picard:2.23.6--0"
-    //container "https://depot.galaxyproject.org/singularity/picard:2.23.6--0"
+    }
-
-    conda (params.conda ? "bioconda::picard=2.23.6" : null)
 
     input:
     tuple val(meta), path(bams)
-    val   options
  
     output:
     tuple val(meta), path("*.bam"), emit: bam
@@ -23,8 +27,7 @@ process PICARD_MERGESAMFILES {
 
     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/picard/mergesamfiles/meta.yml

@@ -23,7 +23,7 @@ params:
         description: |
             Value for the Nextflow `publishDir` mode parameter.
             Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - conda:
+    - enable_conda:
         type: boolean
         description: |
             Run the module with Conda using the software specified
@@ -38,11 +38,6 @@ input:
         type: file
         description: List of BAM files
         pattern: "*.{bam}"
-    - options:
-        type: map
-        description: |
-            Groovy Map containing module options for passing command-line arguments and
-            output file paths.
 output:
     - meta:
         type: map

software/picard/mergesamfiles/test/main.nf

@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { PICARD_MERGESAMFILES } from '../main.nf'
+include { PICARD_MERGESAMFILES } from '../main.nf' addParams( options: [:] )
 
 workflow test {
 
@@ -11,7 +11,7 @@ workflow test {
               [ file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true),
                 file("${baseDir}/input/test.paired_end.COPY.sorted.bam", checkIfExists: true), ] ]
 
-    PICARD_MERGESAMFILES ( input, [:] )
+    PICARD_MERGESAMFILES ( input )
 }
 
 workflow {

software/picard/mergesamfiles/test/nextflow.config

@@ -2,12 +2,12 @@
 params {
     outdir = "output/"
     publish_dir_mode = "copy"
-    conda = false
+    enable_conda = false
 }
 
 profiles {
     conda  {
-        params.conda = true
+        params.enable_conda = true
     }
     docker {
         docker.enabled = true

software/preseq/lcextrap/main.nf

@@ -1,22 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::preseq=2.0.3" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/preseq:2.0.3--hf53bd2b_3"
+    } else {
         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
@@ -25,13 +29,12 @@ process PRESEQ_LCEXTRAP {
 
     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 paired_end = meta.single_end ? '' : '-pe'
     """
     preseq \\
         lc_extrap \\
-        $ioptions.args \\
+        $options.args \\
         $paired_end \\
         -output ${prefix}.ccurve.txt \\
         $bam

software/qualimap/rnaseq/main.nf

@@ -1,22 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 process QUALIMAP_RNASEQ {
     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) }
 
+    conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1"
+    } else {
         container "quay.io/biocontainers/qualimap:2.2.2d--1"
-    //container "https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1"
+    }
-
-    conda (params.conda ? "bioconda::qualimap=2.2.2d" : null)
 
     input:
     tuple val(meta), path(bam)
     path  gtf
-    val   options
     
     output:
     tuple val(meta), path("${prefix}"), emit: results
@@ -24,8 +28,7 @@ process QUALIMAP_RNASEQ {
 
     script:
     def software   = getSoftwareName(task.process)
-    def ioptions   = initOptions(options)
+    prefix         = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    prefix         = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     def paired_end = meta.single_end ? '' : '-pe'
     def memory     = task.memory.toGiga() + "G"
 
@@ -42,7 +45,7 @@ process QUALIMAP_RNASEQ {
     qualimap \\
         --java-mem-size=$memory \\
         rnaseq \\
-        $ioptions.args \\
+        $options.args \\
         -bam $bam \\
         -gtf $gtf \\
         -p $strandedness \\

software/rsem/calculateexpression/main.nf

@@ -1,22 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 process RSEM_CALCULATEEXPRESSION {
     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) }
 
+    conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
+    } else {
         container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
-    //container "https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
+    }
-
-    conda (params.conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
 
     input:
     tuple val(meta), path(reads)
     path  index
-    val   options
     
     output:
     tuple val(meta), path("*.genes.results")   , emit: counts_gene
@@ -31,8 +35,7 @@ process RSEM_CALCULATEEXPRESSION {
 
     script:
     def software   = getSoftwareName(task.process)
-    def ioptions   = initOptions(options)
+    prefix         = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    prefix         = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
 
     def strandedness = ''
     if (meta.strandedness == 'forward') {
@@ -48,7 +51,7 @@ process RSEM_CALCULATEEXPRESSION {
         --temporary-folder ./tmp/ \\
         $strandedness \\
         $paired_end \\
-        $ioptions.args \\
+        $options.args \\
         $reads \\
         \$INDEX \\
         $prefix

software/rsem/preparereference/main.nf

@@ -1,22 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 process RSEM_PREPAREREFERENCE {
     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:'') }
 
+    conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
+    } else {
         container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
-    //container "https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
+    }
-
-    conda (params.conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
 
     input:
     path fasta
     path gtf
-    val  options
     
     output:
     path "rsem"         , emit: index
@@ -24,13 +28,12 @@ process RSEM_PREPAREREFERENCE {
 
     script:
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
     """
     mkdir rsem
     rsem-prepare-reference \\
         --gtf $gtf \\
         --num-threads $task.cpus \\
-        $ioptions.args \\
+        $options.args \\
         $fasta \\
         rsem/genome
 

software/rseqc/bamstat/main.nf

@@ -1,21 +1,25 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 process RSEQC_BAMSTAT {
     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) }
 
+    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    } else {
         container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
-    //container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    }
-
-    conda (params.conda ? "bioconda::rseqc=3.0.1" : null)
 
     input:
     tuple val(meta), path(bam)
-    val   options
     
     output:
     tuple val(meta), path("*.bam_stat.txt"), emit: txt
@@ -23,12 +27,11 @@ process RSEQC_BAMSTAT {
 
     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}"
     """
     bam_stat.py \\
         -i $bam \\
-        $ioptions.args \\
+        $options.args \\
         > ${prefix}.bam_stat.txt
 
     bam_stat.py --version | sed -e "s/bam_stat.py //g" > ${software}.version.txt

software/rseqc/inferexperiment/main.nf

@@ -1,22 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 process RSEQC_INFEREXPERIMENT {
     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) }
 
+    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    } else {
         container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
-    //container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    }
-
-    conda (params.conda ? "bioconda::rseqc=3.0.1" : null)
 
     input:
     tuple val(meta), path(bam)
     path  bed
-    val   options
     
     output:
     tuple val(meta), path("*.infer_experiment.txt"), emit: txt
@@ -24,13 +28,12 @@ process RSEQC_INFEREXPERIMENT {
 
     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}"
     """
     infer_experiment.py \\
         -i $bam \\
         -r $bed \\
-        $ioptions.args \\
+        $options.args \\
         > ${prefix}.infer_experiment.txt
 
     infer_experiment.py --version | sed -e "s/infer_experiment.py //g" > ${software}.version.txt

software/rseqc/innerdistance/main.nf

@@ -1,22 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 process RSEQC_INNERDISTANCE {
     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) }
 
+    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    } else {
         container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
-    //container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    }
-
-    conda (params.conda ? "bioconda::rseqc=3.0.1" : null)
 
     input:
     tuple val(meta), path(bam)
     path  bed
-    val   options
     
     output:
     tuple val(meta), path("*distance.txt"), optional:true, emit: distance
@@ -28,15 +32,14 @@ process RSEQC_INNERDISTANCE {
 
     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}"
     if (!meta.single_end) {
         """
         inner_distance.py \\
             -i $bam \\
             -r $bed \\
             -o $prefix \\
-            $ioptions.args \\
+            $options.args \\
             > stdout.txt
         head -n 2 stdout.txt > ${prefix}.inner_distance_mean.txt
 

software/rseqc/junctionannotation/main.nf

@@ -1,22 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 process RSEQC_JUNCTIONANNOTATION {
     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) }
 
+    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    } else {
         container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
-    //container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    }
-
-    conda (params.conda ? "bioconda::rseqc=3.0.1" : null)
 
     input:
     tuple val(meta), path(bam)
     path  bed
-    val   options
     
     output:
     tuple val(meta), path("*.junction.bed"), emit: bed
@@ -30,14 +34,13 @@ process RSEQC_JUNCTIONANNOTATION {
 
     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}"
     """
     junction_annotation.py \\
         -i $bam \\
         -r $bed \\
         -o $prefix \\
-        $ioptions.args \\
+        $options.args \\
         2> ${prefix}.junction_annotation.log
 
     junction_annotation.py --version | sed -e "s/junction_annotation.py //g" > ${software}.version.txt

software/rseqc/junctionsaturation/main.nf

@@ -1,22 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 process RSEQC_JUNCTIONSATURATION {
     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) }
 
+    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    } else {
         container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
-    //container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    }
-
-    conda (params.conda ? "bioconda::rseqc=3.0.1" : null)
 
     input:
     tuple val(meta), path(bam)
     path  bed
-    val   options
     
     output:
     tuple val(meta), path("*.pdf"), emit: pdf
@@ -25,14 +29,13 @@ process RSEQC_JUNCTIONSATURATION {
 
     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}"
     """
     junction_saturation.py \\
         -i $bam \\
         -r $bed \\
         -o $prefix \\
-        $ioptions.args
+        $options.args
 
     junction_saturation.py --version | sed -e "s/junction_saturation.py //g" > ${software}.version.txt
     """

software/rseqc/readdistribution/main.nf

@@ -1,22 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 process RSEQC_READDISTRIBUTION {
     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) }
 
+    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    } else {
         container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
-    //container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    }
-
-    conda (params.conda ? "bioconda::rseqc=3.0.1" : null)
 
     input:
     tuple val(meta), path(bam)
     path  bed
-    val   options
     
     output:
     tuple val(meta), path("*.read_distribution.txt"), emit: txt
@@ -24,8 +28,7 @@ process RSEQC_READDISTRIBUTION {
 
     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}"
     """
     read_distribution.py \\
         -i $bam \\

software/rseqc/readduplication/main.nf

@@ -1,21 +1,25 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 process RSEQC_READDUPLICATION {
     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) }
 
+    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    } else {
         container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
-    //container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    }
-
-    conda (params.conda ? "bioconda::rseqc=3.0.1" : null)
 
     input:
     tuple val(meta), path(bam)
-    val   options
     
     output:
     tuple val(meta), path("*seq.DupRate.xls"), emit: seq_xls
@@ -26,13 +30,12 @@ process RSEQC_READDUPLICATION {
 
     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}"
     """
     read_duplication.py \\
         -i $bam \\
         -o $prefix \\
-        $ioptions.args
+        $options.args
 
     read_duplication.py --version | sed -e "s/read_duplication.py //g" > ${software}.version.txt
     """

software/salmon/index/main.nf

@@ -1,21 +1,25 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 process SALMON_INDEX {
     tag "$fasta"
     label "process_medium"
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
+    conda (params.enable_conda ? "bioconda::salmon=1.3.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/salmon:1.3.0--hf69c8f4_0"
+    } else {
         container "quay.io/biocontainers/salmon:1.3.0--hf69c8f4_0"
-    //container "https://depot.galaxyproject.org/singularity/salmon:1.3.0--hf69c8f4_0"
+    }
-
-    conda (params.conda ? "bioconda::salmon=1.3.0" : null)
 
     input:
     path fasta
-    val  options
 
     output:
     path "salmon"       , emit: index
@@ -23,13 +27,12 @@ process SALMON_INDEX {
 
     script:
     def software = getSoftwareName(task.process) 
-    def ioptions = initOptions(options)
     """
     salmon \\
         index \\
         --threads $task.cpus \\
         -t $fasta \\
-        $ioptions.args \\
+        $options.args \\
         -i salmon
     salmon --version | sed -e "s/salmon //g" > ${software}.version.txt
     """

software/salmon/quant/main.nf

@@ -1,23 +1,27 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 process SALMON_QUANT {
     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) }
 
+    conda (params.enable_conda ? "bioconda::salmon=1.3.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/salmon:1.3.0--hf69c8f4_0"
+    } else {
         container "quay.io/biocontainers/salmon:1.3.0--hf69c8f4_0"
-    //container "https://depot.galaxyproject.org/singularity/salmon:1.3.0--hf69c8f4_0"
+    }
-
-    conda (params.conda ? "bioconda::salmon=1.3.0" : null)
 
     input:
     tuple val(meta), path(reads)
     path  index
     path  gtf
-    val   options
     
     output:
     tuple val(meta), path("${prefix}"), emit: results
@@ -25,8 +29,7 @@ process SALMON_QUANT {
 
     script:
     def software  = getSoftwareName(task.process)
-    def ioptions  = initOptions(options)
+    prefix        = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    prefix        = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     def endedness = meta.single_end ? "-r $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
 
     def strandedness = meta.single_end ? 'U' : 'IU'
@@ -42,7 +45,7 @@ process SALMON_QUANT {
         --libType=$strandedness \\
         --index $index \\
         $endedness \\
-        $ioptions.args \\
+        $options.args \\
         -o $prefix
 
     salmon --version | sed -e "s/salmon //g" > ${software}.version.txt

software/samtools/flagstat/main.nf

@@ -1,20 +1,23 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
 
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+    } else {
         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

software/samtools/flagstat/meta.yml

@@ -27,7 +27,7 @@ params:
         description: |
             Value for the Nextflow `publishDir` mode parameter.
             Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - conda:
+    - enable_conda:
         type: boolean
         description: |
             Run the module with Conda using the software specified
@@ -46,11 +46,6 @@ input:
         type: file
         description: Index for BAM/CRAM/SAM file
         pattern: "*.{bai,crai,sai}"
-    - options:
-        type: map
-        description: |
-            Groovy Map containing module options for passing command-line arguments and
-            output file paths.
 output:
     - meta:
         type: map

software/samtools/flagstat/test/main.nf

@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { SAMTOOLS_FLAGSTAT } from '../main.nf'
+include { SAMTOOLS_FLAGSTAT } from '../main.nf' addParams( options: [:] )
 
 workflow test {
 
@@ -11,7 +11,7 @@ workflow test {
               file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true),
               file("${baseDir}/input/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
 
-    SAMTOOLS_FLAGSTAT ( input, [:] )
+    SAMTOOLS_FLAGSTAT ( input )
 }
 
 workflow {

software/samtools/flagstat/test/nextflow.config

@@ -2,12 +2,12 @@
 params {
     outdir = "output/"
     publish_dir_mode = "copy"
-    conda = false
+    enable_conda = false
 }
 
 profiles {
     conda  {
-        params.conda = true
+        params.enable_conda = true
     }
     docker {
         docker.enabled = true

software/samtools/idxstats/main.nf

@@ -1,20 +1,23 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
 
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+    } else {
         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

software/samtools/idxstats/meta.yml

@@ -28,7 +28,7 @@ params:
         description: |
             Value for the Nextflow `publishDir` mode parameter.
             Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - conda:
+    - enable_conda:
         type: boolean
         description: |
             Run the module with Conda using the software specified
@@ -47,11 +47,6 @@ input:
         type: file
         description: Index for BAM/CRAM/SAM file
         pattern: "*.{bai,crai,sai}"
-    - options:
-        type: map
-        description: |
-            Groovy Map containing module options for passing command-line arguments and
-            output file paths.
 output:
     - meta:
         type: map

software/samtools/idxstats/test/main.nf

@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { SAMTOOLS_IDXSTATS } from '../main.nf'
+include { SAMTOOLS_IDXSTATS } from '../main.nf' addParams( options: [:] )
 
 workflow test {
 
@@ -11,7 +11,7 @@ workflow test {
               file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true),
               file("${baseDir}/input/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
 
-    SAMTOOLS_IDXSTATS ( input, [:] )
+    SAMTOOLS_IDXSTATS ( input )
 }
 
 workflow {

software/samtools/idxstats/test/nextflow.config

@@ -2,12 +2,12 @@
 params {
     outdir = "output/"
     publish_dir_mode = "copy"
-    conda = false
+    enable_conda = false
 }
 
 profiles {
     conda  {
-        params.conda = true
+        params.enable_conda = true
     }
     docker {
         docker.enabled = true

software/samtools/index/main.nf

@@ -1,20 +1,23 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
 
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+    } else {
         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

software/samtools/index/meta.yml

@@ -25,7 +25,7 @@ params:
         description: |
             Value for the Nextflow `publishDir` mode parameter.
             Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - conda:
+    - enable_conda:
         type: boolean
         description: |
             Run the module with Conda using the software specified
@@ -40,11 +40,6 @@ input:
         type: file
         description: BAM/CRAM/SAM file
         pattern: "*.{bam,cram,sam}"
-    - options:
-        type: map
-        description: |
-            Groovy Map containing module options for passing command-line arguments and
-            output file paths.
 output:
     - meta:
         type: map

software/samtools/index/test/main.nf

@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { SAMTOOLS_INDEX } from '../main.nf'
+include { SAMTOOLS_INDEX } from '../main.nf' addParams( options: [:] )
 
 workflow test {
 
@@ -10,7 +10,7 @@ workflow test {
     input = [ [ id:'test', single_end:false ], // meta map
               file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true) ]
 
-    SAMTOOLS_INDEX ( input, [:] )
+    SAMTOOLS_INDEX ( input )
 }
 
 workflow {

software/samtools/index/test/nextflow.config

@@ -2,12 +2,12 @@
 params {
     outdir = "output/"
     publish_dir_mode = "copy"
-    conda = false
+    enable_conda = false
 }
 
 profiles {
     conda  {
-        params.conda = true
+        params.enable_conda = true
     }
     docker {
         docker.enabled = true

software/samtools/sort/main.nf

@@ -1,21 +1,25 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+    } else {
         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
@@ -23,10 +27,9 @@ process SAMTOOLS_SORT {
 
     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}"
     """
-    samtools sort $ioptions.args -@ $task.cpus -o ${prefix}.bam -T $prefix $bam
+    samtools sort $options.args -@ $task.cpus -o ${prefix}.bam -T $prefix $bam
     echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
     """
 }

software/samtools/sort/meta.yml

@@ -25,7 +25,7 @@ params:
         description: |
             Value for the Nextflow `publishDir` mode parameter.
             Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - conda:
+    - enable_conda:
         type: boolean
         description: |
             Run the module with Conda using the software specified
@@ -40,11 +40,6 @@ input:
         type: file
         description: BAM/CRAM/SAM file
         pattern: "*.{bam,cram,sam}"
-    - options:
-        type: map
-        description: |
-            Groovy Map containing module options for passing command-line arguments and
-            output file paths.
 output:
     - meta:
         type: map

software/samtools/sort/test/main.nf

@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { SAMTOOLS_SORT } from '../main.nf'
+include { SAMTOOLS_SORT } from '../main.nf' addParams( options: [:] )
 
 workflow test {
 
@@ -10,7 +10,7 @@ workflow test {
     input = [ [ id:'test', single_end:false ], // meta map
               file("${baseDir}/input/test.paired_end.name.sorted.bam", checkIfExists: true) ]
 
-    SAMTOOLS_SORT ( input, [:] )
+    SAMTOOLS_SORT ( input )
 }
 
 workflow {

software/samtools/sort/test/nextflow.config

@@ -2,12 +2,12 @@
 params {
     outdir = "output/"
     publish_dir_mode = "copy"
-    conda = false
+    enable_conda = false
 }
 
 profiles {
     conda  {
-        params.conda = true
+        params.enable_conda = true
     }
     docker {
         docker.enabled = true

software/samtools/stats/main.nf

@@ -1,20 +1,23 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
 
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+    } else {
         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

software/samtools/stats/meta.yml

@@ -26,7 +26,7 @@ params:
         description: |
             Value for the Nextflow `publishDir` mode parameter.
             Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - conda:
+    - enable_conda:
         type: boolean
         description: |
             Run the module with Conda using the software specified
@@ -45,11 +45,6 @@ input:
         type: file
         description: Index for BAM/CRAM/SAM file
         pattern: "*.{bai,crai,sai}"
-    - options:
-        type: map
-        description: |
-            Groovy Map containing module options for passing command-line arguments and
-            output file paths.
 output:
     - meta:
         type: map

software/samtools/stats/test/main.nf

@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { SAMTOOLS_STATS } from '../main.nf'
+include { SAMTOOLS_STATS } from '../main.nf' addParams( options: [:] )
 
 workflow test {
 
@@ -11,7 +11,7 @@ workflow test {
               file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true),
               file("${baseDir}/input/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
 
-    SAMTOOLS_STATS ( input, [:] )
+    SAMTOOLS_STATS ( input )
 }
 
 workflow {

software/samtools/stats/test/nextflow.config

@@ -2,12 +2,12 @@
 params {
     outdir = "output/"
     publish_dir_mode = "copy"
-    conda = false
+    enable_conda = false
 }
 
 profiles {
     conda  {
-        params.conda = true
+        params.enable_conda = true
     }
     docker {
         docker.enabled = true

software/sortmerna/main.nf

@@ -1,22 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 process SORTMERNA {
     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) }
 
+    conda (params.enable_conda ? "bioconda::sortmerna=4.2.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/sortmerna:4.2.0--0"
+    } else {
         container "quay.io/biocontainers/sortmerna:4.2.0--0"
-    //container "https://depot.galaxyproject.org/singularity/sortmerna:4.2.0--0"
+    }
-
-    conda (params.conda ? "bioconda::sortmerna=4.2.0" : null)
 
     input:
     tuple val(meta), path(reads)
     path  fasta
-    val   options
     
     output:
     tuple val(meta), path("*.fastq.gz"), emit: reads
@@ -25,8 +29,7 @@ process SORTMERNA {
 
     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 Refs = ""
     for (i=0; i<fasta.size(); i++) { Refs+= " --ref ${fasta[i]}" }
@@ -39,7 +42,7 @@ process SORTMERNA {
             --workdir . \\
             --aligned rRNA_reads \\
             --other non_rRNA_reads \\
-            $ioptions.args
+            $options.args
 
         gzip -f < non_rRNA_reads.fq > ${prefix}.fastq.gz
         mv rRNA_reads.log ${prefix}.sortmerna.log
@@ -58,7 +61,7 @@ process SORTMERNA {
             --other non_rRNA_reads \\
             --paired_in \\
             --out2 \\
-            $ioptions.args
+            $options.args
 
         gzip -f < non_rRNA_reads_fwd.fq > ${prefix}_1.fastq.gz
         gzip -f < non_rRNA_reads_rev.fq > ${prefix}_2.fastq.gz

software/star/align/main.nf

@@ -1,24 +1,28 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 process STAR_ALIGN {
     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) }
 
-    // Don't upgrade me - 2.7X indices incompatible with iGenomes.
+    // Note: 2.7X indices incompatible with AWS iGenomes.
+    conda (params.enable_conda ? "bioconda::star=2.6.1d" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/star:2.6.1d--0"
+    } else {
         container "quay.io/biocontainers/star:2.6.1d--0"
-    //container "https://depot.galaxyproject.org/singularity/star:2.6.1d--0"
+    }
-
-    conda (params.conda ? "bioconda::star=2.6.1d" : null)
 
     input:
     tuple val(meta), path(reads)
     path  index
     path  gtf
-    val   options
     
     output:
     tuple val(meta), path("*Aligned.out.bam") , emit: bam
@@ -34,8 +38,7 @@ process STAR_ALIGN {
 
     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 ignore_gtf = params.star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf"
     def seq_center = params.seq_center ? "--outSAMattrRGline ID:$prefix 'CN:$params.seq_center' 'SM:$prefix'" : "--outSAMattrRGline ID:$prefix 'SM:$prefix'"
     """
@@ -46,7 +49,7 @@ process STAR_ALIGN {
         --outFileNamePrefix $prefix. \\
         $ignore_gtf \\
         $seq_center \\
-        $ioptions.args
+        $options.args
 
     if [ -f ${prefix}.Unmapped.out.mate1 ]; then
         mv ${prefix}.Unmapped.out.mate1 ${prefix}.unmapped_1.fastq

software/star/genomegenerate/main.nf

@@ -1,23 +1,27 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 process STAR_GENOMEGENERATE {
     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:'') }
 
-    // Don't upgrade me - 2.7X indices incompatible with iGenomes.
+    // Note: 2.7X indices incompatible with AWS iGenomes.
+    conda (params.enable_conda ? "bioconda::star=2.6.1d" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/star:2.6.1d--0"
+    } else {
         container "quay.io/biocontainers/star:2.6.1d--0"
-    //container "https://depot.galaxyproject.org/singularity/star:2.6.1d--0"
+    }
-
-    conda (params.conda ? "bioconda::star=2.6.1d" : null)
 
     input:
     path fasta
     path gtf
-    val  options
 
     output:
     path "star"         , emit: index
@@ -25,7 +29,6 @@ process STAR_GENOMEGENERATE {
 
     script:
     def software  = getSoftwareName(task.process)
-    def ioptions  = initOptions(options)
     def memory    = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
     """
     mkdir star
@@ -36,7 +39,7 @@ process STAR_GENOMEGENERATE {
         --sjdbGTFfile $gtf \\
         --runThreadN $task.cpus \\
         $memory \\
-        $ioptions.args
+        $options.args
 
     STAR --version | sed -e "s/STAR_//g" > ${software}.version.txt
     """

software/stringtie/main.nf

@@ -1,22 +1,27 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 process STRINGTIE {
     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) }
 
+    // Note: 2.7X indices incompatible with AWS iGenomes.
+    conda (params.enable_conda ? "bioconda::stringtie=2.1.4" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/stringtie:2.1.4--h7e0af3c_0"
+    } else {
         container "quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0"
-    //container "https://depot.galaxyproject.org/singularity/stringtie:2.1.4--h7e0af3c_0"
+    }
-
-    conda (params.conda ? "bioconda::stringtie=2.1.4" : null)
 
     input:
     tuple val(meta), path(bam)
     path  gtf
-    val   options
     
     output:
     tuple val(meta), path("*.coverage.gtf")   , emit: coverage_gtf
@@ -27,8 +32,7 @@ process STRINGTIE {
 
     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 strandedness = ''
     if (meta.strandedness == 'forward') {
@@ -45,7 +49,7 @@ process STRINGTIE {
         -A ${prefix}.gene_abundance.txt \\
         -C ${prefix}.coverage.gtf \\
         -b ${prefix}.ballgown \\
-        $ioptions.args
+        $options.args
 
     stringtie --version > ${software}.version.txt
     """

software/subread/featurecounts/main.nf

@@ -1,21 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    // Note: 2.7X indices incompatible with AWS iGenomes.
+    conda (params.enable_conda ? "bioconda::subread=2.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/subread:2.0.1--hed695b0_0"
+    } else {
         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: counts
@@ -24,8 +29,7 @@ process SUBREAD_FEATURECOUNTS {
 
     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 paired_end = meta.single_end ? '' : '-p'
 
     def strandedness = 0
@@ -36,7 +40,7 @@ process SUBREAD_FEATURECOUNTS {
     }
     """
     featureCounts \\
-        $ioptions.args \\
+        $options.args \\
         $paired_end \\
         -T $task.cpus \\
         -a $annotation \\

software/trimgalore/main.nf

@@ -1,21 +1,25 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::trim-galore=0.6.6" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.6--0"
+    } else {
         container "quay.io/biocontainers/trim-galore:0.6.6--0"
-    //container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.6--0"
+    }
-
-    conda (params.conda ? "bioconda::trim-galore=0.6.6" : null)
 
     input:
     tuple val(meta), path(reads)
-    val   options
 
     output:
     tuple val(meta), path("*.fq.gz")    , emit: reads
@@ -45,13 +49,12 @@ process TRIMGALORE {
 
     // Added soft-links to original fastqs for consistent naming in MultiQC
     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}"
     if (meta.single_end) {
         """
         [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
         trim_galore \\
-            $ioptions.args \\
+            $options.args \\
             --cores $cores \\
             --gzip \\
             $c_r1 \\
@@ -64,7 +67,7 @@ process TRIMGALORE {
         [ ! -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 \\
+            $options.args \\
             --cores $cores \\
             --paired \\
             --gzip \\

software/trimgalore/meta.yml

@@ -24,7 +24,7 @@ params:
         description: |
             Value for the Nextflow `publishDir` mode parameter.
             Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - conda:
+    - enable_conda:
         type: boolean
         description: |
             Run the module with Conda using the software specified
@@ -60,11 +60,6 @@ input:
         description: |
             List of input FastQ files of size 1 and 2 for single-end and paired-end data,
             respectively.
-    - options:
-        type: map
-        description: |
-            Groovy Map containing module options for passing command-line arguments and
-            output file paths.
 output:
     - meta:
         type: map

software/trimgalore/test/main.nf

@@ -2,7 +2,8 @@
 
 nextflow.enable.dsl = 2
 
-include { TRIMGALORE } from '../main.nf'
+include { TRIMGALORE as TRIMGALORE_SE } from '../main.nf'  addParams( options: [ publish_dir:'test_single_end' ] )
+include { TRIMGALORE as TRIMGALORE_PE } from '../main.nf'  addParams( options: [ publish_dir:'test_paired_end' ] )
 
 /*
  * Test with single-end data
@@ -13,7 +14,7 @@ workflow test_single_end {
     input = [ [ id:'test', single_end:true ], // meta map
               [ file("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ]
 
-    TRIMGALORE ( input, [ publish_dir:'test_single_end' ] )
+    TRIMGALORE_SE ( input )
 }
 
 /*
@@ -26,7 +27,7 @@ workflow test_paired_end {
               [ file("${baseDir}/input/test_R1.fastq.gz", checkIfExists: true),
                 file("${baseDir}/input/test_R2.fastq.gz", checkIfExists: true) ] ]
 
-    TRIMGALORE ( input, [ publish_dir:'test_paired_end' ] )
+    TRIMGALORE_PE ( input )
 }
 
 workflow {

software/trimgalore/test/nextflow.config

@@ -2,7 +2,7 @@
 params {
     outdir = "output/"
     publish_dir_mode = "copy"
-    conda = false
+    enable_conda = false
 
     clip_r1 = 0
     clip_r2 = 0
@@ -12,7 +12,7 @@ params {
 
 profiles {
     conda  {
-        params.conda = true
+        params.enable_conda = true
     }
     docker {
         docker.enabled = true

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 {
@@ -8,17 +11,18 @@ 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) }
 
+    conda (params.enable_conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:377--h446ed27_1"
+    } else {
         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
@@ -26,8 +30,7 @@ process UCSC_BEDRAPHTOBIGWIG {
 
     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

software/umitools/dedup/main.nf

@@ -1,21 +1,25 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 process UMITOOLS_DEDUP {
     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) }
 
+    conda (params.enable_conda ? "bioconda::umi_tools=1.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/umi_tools:1.0.1--py37h516909a_1"
+    } else {
         container "quay.io/biocontainers/umi_tools:1.0.1--py37h516909a_1"
-    //container "https://depot.galaxyproject.org/singularity/umi_tools:1.0.1--py37h516909a_1"
+    }
-
-    conda (params.conda ? "bioconda::umi_tools=1.0.1" : null)
 
     input:
     tuple val(meta), path(bam), path(bai)
-    val   options
     
     output:
     tuple val(meta), path("*.bam"), emit: bam
@@ -24,14 +28,13 @@ process UMITOOLS_DEDUP {
 
     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}"
     """
     umi_tools dedup \\
         -I $bam \\
         -S ${prefix}.bam \\
         --output-stats=$prefix \\
-        $ioptions.args \\
+        $options.args \\
 
     umi_tools --version | sed -e "s/UMI-tools version: //g" > ${software}.version.txt
     """

software/umitools/extract/main.nf

@@ -1,21 +1,25 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 process UMITOOLS_EXTRACT {
     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) }
 
+    conda (params.enable_conda ? "bioconda::umi_tools=1.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/umi_tools:1.0.1--py37h516909a_1"
+    } else {
         container "quay.io/biocontainers/umi_tools:1.0.1--py37h516909a_1"
-    //container "https://depot.galaxyproject.org/singularity/umi_tools:1.0.1--py37h516909a_1"
+    }
-
-    conda (params.conda ? "bioconda::umi_tools=1.0.1" : null)
 
     input:
     tuple val(meta), path(reads)
-    val   options
 
     output:
     tuple val(meta), path("*.fastq.gz"), emit: reads
@@ -24,15 +28,14 @@ process UMITOOLS_EXTRACT {
 
     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}"
     if (meta.single_end) {
         """
         umi_tools \\
             extract \\
             -I $reads \\
             -S ${prefix}.umi_extract.fastq.gz \\
-            $ioptions.args \\
+            $options.args \\
             > ${prefix}.umi_extract.log
 
         umi_tools --version | sed -e "s/UMI-tools version: //g" > ${software}.version.txt
@@ -45,7 +48,7 @@ process UMITOOLS_EXTRACT {
             --read2-in=${reads[1]} \\
             -S ${prefix}.umi_extract_1.fastq.gz \\
             --read2-out=${prefix}.umi_extract_2.fastq.gz \\
-            $ioptions.args \\
+            $options.args \\
             > ${prefix}.umi_extract.log
 
         umi_tools --version | sed -e "s/UMI-tools version: //g" > ${software}.version.txt