Update all modules to new NF DSL2 syntax (#1099)

* Add comment line for consistency

* Remove all functions.nf

* Remove include functions.nf and publishDir options

* Replace options.args3 with task.ext.args3 - 3 modules

* Replace options.args3 with task.ext.args3 - 17 modules

* Replace {task.cpus} with task.cpus

* Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with

* Add def args = task.ext.args line to all modules in script section

* Replace options.args with args and args_list

* Initialise args2 and args3 properly

* Replace container syntax

* Revert container changes for cellranger/mkref

* Replace getProcessName in all modules

* Replace getSoftwareName in all modules

* Unify modules using VERSION variable

* Replae options.suffix with task.ext.suffix

* Remove NF version restriction for CI

* Bump NF version in README

* Replace task.process.tokenize logic with task.process

* Minor tweaks to unify syntax in tests main.nf

* Add a separate nextflow.config for each module

* Transfer remaining module options to nextflow.config

* Remove addParams from tests main.nf

* Remove TODO statements

* Use -c to import module specific config

* Bump NF version to 21.10.3

* Fix tests for artic/minion

* Fix broken publishDir syntax

* Standardise and fix obvious failing module tests

* Remove kronatools to krona

* Comment out tags in subworkflow test.yml

* Fix failing module tests

* Add consistent indentation to nextflow.config

* Comment out subworklow definitions

* Fix kallistobustools/ref

* Fix rmarkdownnotebook

* Fix jupyternotebook

* Quote task.process

* Add plink2/vcf to pytest_modules.yml

* Remove NF_CORE_MODULES_TEST from pytest CI

* Fix more tests

* Move bacteroides_fragilis to prokaryotes folder

* Fix cooler merge tests

* Fix kallistobustools/count tests

* Fix kallistobustools/ref tests

* Update test_10x_1_fastq_gz file for kallistobustools/count tests

* Fix bcftools/query tests

* Fix delly/call tests

* Fix cooler/zoomify tests

* Fix csvtk/split tests

* Fix gatk4/intervallisttools tests

* Fix gatk4/variantfiltration

* Fix pydamage/filter tests

* Fix test data for unicycler

* Fix gstama/collapse module

* Fix leehom tests

* Fix metaphlan3 tests

* Fix pairtools/select tests

* Update nextflow.config

* Update nextflow.config

* feat: update syntax

* Fix arriba tests

* Fix more failing tests

* Update test syntax

* Remove comments from tests nextflow.config

* Apply suggestions from code review

* Fix kallistobustools/count module

* Update dumpsoftwareversions module

* Update custom/dumpsoftwareversions

* Add args2 to untar module

* Update leftover modules

* Remove last remaining addParams

Co-authored-by: JoseEspinosa <kadomu@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>

.github/workflows/nf-core-linting.yml

@@ -7,7 +7,6 @@ on:
   pull_request:
     branches: [master]
 
-
 jobs:
   changes:
     name: Check for changes
@@ -25,9 +24,6 @@ jobs:
 
   lint:
     runs-on: ubuntu-20.04
-    env:
-      NXF_VER: 21.04.0
-
     name: ${{ matrix.tags }}
     needs: changes
     if: needs.changes.outputs.modules != '[]'

.github/workflows/pytest-workflow.yml

@@ -23,13 +23,12 @@ jobs:
   test:
     runs-on: ubuntu-20.04
 
-    name: ${{ matrix.tags }} ${{ matrix.profile }} ${{ matrix.nxf_version }}
+    name: ${{ matrix.tags }} ${{ matrix.profile }}
     needs: changes
     if: needs.changes.outputs.modules != '[]'
     strategy:
       fail-fast: false
       matrix:
-        nxf_version: ["21.04.0"]
         tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
         profile: ["docker", "singularity", "conda"]
     env:
@@ -60,13 +59,12 @@ jobs:
       - uses: actions/cache@v2
         with:
           path: /usr/local/bin/nextflow
-          key: ${{ runner.os }}-nextflow-${{ matrix.nxf_version }}
+          key: ${{ runner.os }}
           restore-keys: |
             ${{ runner.os }}-nextflow-
 
       - name: Install Nextflow
         env:
-          NXF_VER: ${{ matrix.nxf_version }}
           CAPSULE_LOG: none
         run: |
           wget -qO- get.nextflow.io | bash
@@ -93,13 +91,13 @@ jobs:
       # Test the module
       - name: Run pytest-workflow
         # only use one thread for pytest-workflow to avoid race condition on conda cache.
-        run: NF_CORE_MODULES_TEST=1 TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof
+        run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof
 
       - name: Upload logs on failure
         if: failure()
         uses: actions/upload-artifact@v2
         with:
-          name: logs-${{ matrix.profile }}-${{ matrix.nxf_version }}
+          name: logs-${{ matrix.profile }}
           path: |
             /home/runner/pytest_workflow_*/*/.nextflow.log
             /home/runner/pytest_workflow_*/*/log.out

README.md

@@ -1,6 +1,6 @@
 # ![nf-core/modules](docs/images/nfcore-modules_logo.png)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.04.0-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
@@ -78,7 +78,7 @@ 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/modules/fastqc/main' addParams( options: [:] )
+    include { FASTQC } from './modules/nf-core/modules/fastqc/main'
     ```
 
 5. Remove the module from the pipeline repository if required:

modules/abacas/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/abacas/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process ABACAS {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::abacas=1.3.1" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/abacas:1.3.1--pl526_0"
+        'https://depot.galaxyproject.org/singularity/abacas:1.3.1--pl526_0' :
-    } else {
+        'quay.io/biocontainers/abacas:1.3.1--pl526_0' }"
-        container "quay.io/biocontainers/abacas:1.3.1--pl526_0"
-    }
 
     input:
     tuple val(meta), path(scaffold)
@@ -27,12 +16,13 @@ process ABACAS {
     path "versions.yml"               , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     """
     abacas.pl \\
         -r $fasta \\
         -q $scaffold \\
-        $options.args \\
+        $args \\
         -o ${prefix}.abacas
 
     mv nucmer.delta ${prefix}.abacas.nucmer.delta
@@ -40,8 +30,8 @@ process ABACAS {
     mv nucmer.tiling ${prefix}.abacas.nucmer.tiling
     mv unused_contigs.out ${prefix}.abacas.unused.contigs.out
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(echo \$(abacas.pl -v 2>&1) | sed 's/^.*ABACAS.//; s/ .*\$//')
+        abacas: \$(echo \$(abacas.pl -v 2>&1) | sed 's/^.*ABACAS.//; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/adapterremoval/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/adapterremoval/main.nf

@@ -1,21 +1,11 @@
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process ADAPTERREMOVAL {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::adapterremoval=2.3.2" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/adapterremoval:2.3.2--hb7ba0dd_0"
+        'https://depot.galaxyproject.org/singularity/adapterremoval:2.3.2--hb7ba0dd_0' :
-    } else {
+        'quay.io/biocontainers/adapterremoval:2.3.2--hb7ba0dd_0' }"
-        container "quay.io/biocontainers/adapterremoval:2.3.2--hb7ba0dd_0"
-    }
 
     input:
     tuple val(meta), path(reads)
@@ -26,13 +16,14 @@ process ADAPTERREMOVAL {
     path "versions.yml"                , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
 
     if (meta.single_end) {
         """
         AdapterRemoval  \\
             --file1 $reads \\
-            $options.args \\
+            $args \\
             --basename $prefix \\
             --threads $task.cpus \\
             --settings ${prefix}.log \\
@@ -41,8 +32,8 @@ process ADAPTERREMOVAL {
             --gzip \\
 
         cat <<-END_VERSIONS > versions.yml
-        ${getProcessName(task.process)}:
+        "${task.process}":
-            ${getSoftwareName(task.process)}: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
+            adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
         END_VERSIONS
         """
     } else if (!meta.single_end && !meta.collapse) {
@@ -50,7 +41,7 @@ process ADAPTERREMOVAL {
         AdapterRemoval  \\
             --file1 ${reads[0]} \\
             --file2 ${reads[1]} \\
-            $options.args \\
+            $args \\
             --basename $prefix \\
             --threads $task.cpus \\
             --settings ${prefix}.log \\
@@ -60,8 +51,8 @@ process ADAPTERREMOVAL {
             --gzip \\
 
         cat <<-END_VERSIONS > versions.yml
-        ${getProcessName(task.process)}:
+        "${task.process}":
-            ${getSoftwareName(task.process)}: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
+            adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
         END_VERSIONS
         """
     } else {
@@ -70,7 +61,7 @@ process ADAPTERREMOVAL {
             --file1 ${reads[0]} \\
             --file2 ${reads[1]} \\
             --collapse \\
-            $options.args \\
+            $args \\
             --basename $prefix \\
             --threads $task.cpus \\
             --settings ${prefix}.log \\
@@ -79,8 +70,8 @@ process ADAPTERREMOVAL {
 
         cat *.collapsed.gz *.collapsed.truncated.gz > ${prefix}.merged.fastq.gz
         cat <<-END_VERSIONS > versions.yml
-        ${getProcessName(task.process)}:
+        "${task.process}":
-            ${getSoftwareName(task.process)}: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
+            adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
         END_VERSIONS
         """
     }

modules/agrvate/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/agrvate/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process AGRVATE {
     tag "$meta.id"
     label 'process_low'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::agrvate=1.0.2" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/agrvate:1.0.2--hdfd78af_0"
+        'https://depot.galaxyproject.org/singularity/agrvate:1.0.2--hdfd78af_0' :
-    } else {
+        'quay.io/biocontainers/agrvate:1.0.2--hdfd78af_0' }"
-        container "quay.io/biocontainers/agrvate:1.0.2--hdfd78af_0"
-    }
 
     input:
     tuple val(meta), path(fasta)
@@ -27,15 +16,16 @@ process AGRVATE {
     path "versions.yml"                                                             , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     """
     agrvate \\
-        $options.args \\
+        $args \\
         -i $fasta
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(echo \$(agrvate -v 2>&1) | sed 's/agrvate v//;')
+        agrvate: \$(echo \$(agrvate -v 2>&1) | sed 's/agrvate v//;')
     END_VERSIONS
     """
 }

modules/allelecounter/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/allelecounter/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process ALLELECOUNTER {
     tag "$meta.id"
     label 'process_low'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? 'bioconda::cancerit-allelecount=4.3.0' : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/cancerit-allelecount:4.3.0--h41abebc_0"
+        'https://depot.galaxyproject.org/singularity/cancerit-allelecount:4.3.0--h41abebc_0' :
-    } else {
+        'quay.io/biocontainers/cancerit-allelecount:4.3.0--h41abebc_0' }"
-        container "quay.io/biocontainers/cancerit-allelecount:4.3.0--h41abebc_0"
-    }
 
     input:
     tuple val(meta), path(input), path(input_index)
@@ -28,20 +17,21 @@ process ALLELECOUNTER {
     path "versions.yml"                   , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     def reference_options = fasta ? "-r $fasta": ""
 
     """
     alleleCounter \\
-        $options.args \\
+        $args \\
         -l $loci \\
         -b $input \\
         $reference_options \\
         -o ${prefix}.alleleCount
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(alleleCounter --version)
+        allelecounter: \$(alleleCounter --version)
     END_VERSIONS
     """
 }

modules/amps/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/amps/main.nf

@@ -1,21 +1,10 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process AMPS {
     label 'process_low'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "bioconda::hops=0.35" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1"
+        'https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1' :
-    } else {
+        'quay.io/biocontainers/hops:0.35--hdfd78af_1' }"
-        container "quay.io/biocontainers/hops:0.35--hdfd78af_1"
-    }
 
     input:
     path maltextract_results
@@ -30,6 +19,7 @@ process AMPS {
     path "versions.yml"                        , emit: versions
 
     script:
+    def args = task.ext.args ?: ''
     """
     postprocessing.AMPS.r \\
         -r $maltextract_results \\
@@ -37,11 +27,11 @@ process AMPS {
         -m $filter \\
         -t $task.cpus \\
         -j \\
-        $options.args
+        $args
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(echo \$(hops --version 2>&1) | sed 's/HOPS version//')
+        amps: \$(echo \$(hops --version 2>&1) | sed 's/HOPS version//')
     END_VERSIONS
     """
 }

modules/arriba/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/arriba/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process ARRIBA {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::arriba=2.1.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/arriba:2.1.0--h3198e80_1"
+        'https://depot.galaxyproject.org/singularity/arriba:2.1.0--h3198e80_1' :
-    } else {
+        'quay.io/biocontainers/arriba:2.1.0--h3198e80_1' }"
-        container "quay.io/biocontainers/arriba:2.1.0--h3198e80_1"
-    }
 
     input:
     tuple val(meta), path(bam)
@@ -29,8 +18,9 @@ process ARRIBA {
     path "versions.yml"                             , emit: versions
 
     script:
-    def prefix    = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
-    def blacklist = (options.args.contains('-b')) ? '' : '-f blacklist'
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
+    def blacklist = (args.contains('-b')) ? '' : '-f blacklist'
     """
     arriba \\
         -x $bam \\
@@ -39,11 +29,11 @@ process ARRIBA {
         -o ${prefix}.fusions.tsv \\
         -O ${prefix}.fusions.discarded.tsv \\
         $blacklist \\
-        $options.args
+        $args
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(arriba -h | grep 'Version:' 2>&1 |  sed 's/Version:\s//')
+        arriba: \$(arriba -h | grep 'Version:' 2>&1 |  sed 's/Version:\s//')
     END_VERSIONS
     """
 }

modules/artic/guppyplex/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/artic/guppyplex/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process ARTIC_GUPPYPLEX {
     tag "$meta.id"
     label 'process_high'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::artic=1.2.1" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/artic:1.2.1--py_0"
+        'https://depot.galaxyproject.org/singularity/artic:1.2.1--py_0' :
-    } else {
+        'quay.io/biocontainers/artic:1.2.1--py_0' }"
-        container "quay.io/biocontainers/artic:1.2.1--py_0"
-    }
 
     input:
     tuple val(meta), path(fastq_dir)
@@ -26,18 +15,19 @@ process ARTIC_GUPPYPLEX {
     path  "versions.yml"               , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     """
     artic \\
         guppyplex \\
-        $options.args \\
+        $args \\
         --directory $fastq_dir \\
         --output ${prefix}.fastq
 
     pigz -p $task.cpus *.fastq
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(artic --version 2>&1 | sed 's/^.*artic //; s/ .*\$//')
+        artic: \$(artic --version 2>&1 | sed 's/^.*artic //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/artic/minion/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/artic/minion/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process ARTIC_MINION {
     tag "$meta.id"
     label 'process_high'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::artic=1.2.1" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/artic:1.2.1--py_0"
+        'https://depot.galaxyproject.org/singularity/artic:1.2.1--py_0' :
-    } else {
+        'quay.io/biocontainers/artic:1.2.1--py_0' }"
-        container "quay.io/biocontainers/artic:1.2.1--py_0"
-    }
 
     input:
     tuple val(meta), path(fastq)
@@ -43,20 +32,21 @@ process ARTIC_MINION {
     path  "versions.yml"                                              , emit: versions
 
     script:
-    prefix       = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     def version  = scheme_version.toString().toLowerCase().replaceAll('v','')
-    def fast5    = params.fast5_dir          ? "--fast5-directory $fast5_dir"             : ""
+    def fast5    = fast5_dir ? "--fast5-directory $fast5_dir"             : ""
-    def summary  = params.sequencing_summary ? "--sequencing-summary $sequencing_summary" : ""
+    def summary  = sequencing_summary ? "--sequencing-summary $sequencing_summary" : ""
     def model    = ""
-    if (options.args.tokenize().contains('--medaka')) {
+    if (args.tokenize().contains('--medaka')) {
         fast5   = ""
         summary = ""
-        model = file(params.artic_minion_medaka_model).exists() ? "--medaka-model ./$medaka_model" : "--medaka-model $params.artic_minion_medaka_model"
+        model = file(medaka_model).exists() ? "--medaka-model ./$medaka_model" : "--medaka-model $medaka_model"
     }
     """
     artic \\
         minion \\
-        $options.args \\
+        $args \\
         --threads $task.cpus \\
         --read-file $fastq \\
         --scheme-directory ./primer-schemes \\
@@ -68,8 +58,8 @@ process ARTIC_MINION {
         $prefix
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(artic --version 2>&1 | sed 's/^.*artic //; s/ .*\$//')
+        artic: \$(artic --version 2>&1 | sed 's/^.*artic //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/assemblyscan/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/assemblyscan/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process ASSEMBLYSCAN {
     tag "$meta.id"
     label 'process_low'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::assembly-scan=0.4.1" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/assembly-scan:0.4.1--pyhdfd78af_0"
+        'https://depot.galaxyproject.org/singularity/assembly-scan:0.4.1--pyhdfd78af_0' :
-    } else {
+        'quay.io/biocontainers/assembly-scan:0.4.1--pyhdfd78af_0' }"
-        container "quay.io/biocontainers/assembly-scan:0.4.1--pyhdfd78af_0"
-    }
 
     input:
     tuple val(meta), path(assembly)
@@ -26,13 +15,14 @@ process ASSEMBLYSCAN {
     path "versions.yml"            , emit: versions
 
     script:
-    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     """
     assembly-scan $assembly > ${prefix}.json
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$( assembly-scan --version 2>&1 | sed 's/^.*assembly-scan //; s/Using.*\$//' )
+        assemblyscan: \$( assembly-scan --version 2>&1 | sed 's/^.*assembly-scan //; s/Using.*\$//' )
     END_VERSIONS
     """
 }

modules/ataqv/ataqv/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/ataqv/ataqv/main.nf

@@ -1,21 +1,11 @@
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process ATAQV_ATAQV {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::ataqv=1.2.1" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/ataqv:1.2.1--py39ha23c084_2"
+        'https://depot.galaxyproject.org/singularity/ataqv:1.2.1--py39ha23c084_2' :
-    } else {
+        'quay.io/biocontainers/ataqv:1.2.1--py36hfdecbe1_2' }"
-        container "quay.io/biocontainers/ataqv:1.2.1--py36hfdecbe1_2"
-    }
 
     input:
     tuple val(meta), path(bam), path(bai), path(peak_file)
@@ -30,14 +20,15 @@ process ATAQV_ATAQV {
     path "versions.yml"                  , emit: versions
 
     script:
-    def prefix      = options.suffix   ? "${meta.id}${options.suffix}"                  : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     def peak        = peak_file        ? "--peak-file $peak_file"                       : ''
     def tss         = tss_file         ? "--tss-file $tss_file"                         : ''
     def excl_regs   = excl_regs_file   ? "--excluded-region-file $excl_regs_file"       : ''
     def autosom_ref = autosom_ref_file ? "--autosomal-reference-file $autosom_ref_file" : ''
     """
     ataqv \\
-        $options.args \\
+        $args \\
         $peak \\
         $tss \\
         $excl_regs \\
@@ -49,8 +40,8 @@ process ATAQV_ATAQV {
         $bam
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$( ataqv --version )
+        ataqv: \$( ataqv --version )
     END_VERSIONS
     """
 }

modules/bakta/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bakta/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BAKTA {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bakta=1.2.2" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bakta:1.2.2--pyhdfd78af_0"
+        'https://depot.galaxyproject.org/singularity/bakta:1.2.2--pyhdfd78af_0' :
-    } else {
+        'quay.io/biocontainers/bakta:1.2.2--pyhdfd78af_0' }"
-        container "quay.io/biocontainers/bakta:1.2.2--pyhdfd78af_0"
-    }
 
     input:
     tuple val(meta), path(fasta)
@@ -37,27 +26,28 @@ process BAKTA {
     path "versions.yml"                                 , emit: versions
 
     script:
-    prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     def proteins_opt = proteins ? "--proteins ${proteins[0]}" : ""
     def prodigal_opt = prodigal_tf ? "--prodigal-tf ${prodigal_tf[0]}" : ""
     """
     bakta \\
-        $options.args \\
+        $args \\
         --threads $task.cpus \\
-        --prefix ${prefix} \\
+        --prefix $prefix \\
         --db $db \\
         $proteins_opt \\
         $prodigal_tf \\
         $fasta
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$( echo \$(bakta --version 2>&1) | sed 's/^.*bakta //' )
+        bakta: \$( echo \$(bakta --version 2>&1) | sed 's/^.*bakta //' )
     END_VERSIONS
     """
 
     stub:
-    prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     """
     touch ${prefix}.embl
     touch ${prefix}.faa
@@ -70,8 +60,8 @@ process BAKTA {
     touch ${prefix}.tsv
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$( echo \$(bakta --version 2>&1) | sed 's/^.*bakta //' )
+        bakta: \$( echo \$(bakta --version 2>&1) | sed 's/^.*bakta //' )
     END_VERSIONS
     """
 }

modules/bamaligncleaner/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bamaligncleaner/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BAMALIGNCLEANER {
     tag "$meta.id"
     label 'process_low'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bamaligncleaner=0.2.1" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bamaligncleaner:0.2.1--pyhdfd78af_0"
+        'https://depot.galaxyproject.org/singularity/bamaligncleaner:0.2.1--pyhdfd78af_0' :
-    } else {
+        'quay.io/biocontainers/bamaligncleaner:0.2.1--pyhdfd78af_0' }"
-        container "quay.io/biocontainers/bamaligncleaner:0.2.1--pyhdfd78af_0"
-    }
 
     input:
     tuple val(meta), path(bam)
@@ -26,17 +15,18 @@ process BAMALIGNCLEANER {
     path "versions.yml"           , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
 
     """
     bamAlignCleaner \\
-        $options.args \\
+        $args \\
         -o ${prefix}.bam \\
         ${bam}
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(bamAlignCleaner --version | sed 's/.*version //')
+        bamaligncleaner: \$(bamAlignCleaner --version | sed 's/.*version //')
     END_VERSIONS
     """
 }

modules/bamtools/split/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bamtools/split/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BAMTOOLS_SPLIT {
     tag "$meta.id"
     label 'process_low'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9"
+        'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' :
-    } else {
+        'quay.io/biocontainers/bamtools:2.5.1--h9a82719_9' }"
-        container "quay.io/biocontainers/bamtools:2.5.1--h9a82719_9"
-    }
 
     input:
     tuple val(meta), path(bam)
@@ -26,16 +15,17 @@ process BAMTOOLS_SPLIT {
     path "versions.yml"           , emit: versions
 
     script:
-    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     """
     bamtools \\
         split \\
         -in $bam \\
-        $options.args
+        $args
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$( bamtools --version | grep -e 'bamtools' | sed 's/^.*bamtools //' )
+        bamtools: \$( bamtools --version | grep -e 'bamtools' | sed 's/^.*bamtools //' )
     END_VERSIONS
     """
 }

modules/bamutil/trimbam/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bamutil/trimbam/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BAMUTIL_TRIMBAM {
     tag "$meta.id"
     label 'process_low'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bamutil=1.0.15" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bamutil:1.0.15--h2e03b76_1"
+        'https://depot.galaxyproject.org/singularity/bamutil:1.0.15--h2e03b76_1' :
-    } else {
+        'quay.io/biocontainers/bamutil:1.0.15--h2e03b76_1' }"
-        container "quay.io/biocontainers/bamutil:1.0.15--h2e03b76_1"
-    }
 
     input:
     tuple val(meta), path(bam), val(trim_left), val(trim_right)
@@ -26,19 +15,20 @@ process BAMUTIL_TRIMBAM {
     path "versions.yml"           , emit: versions
 
     script:
-    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     """
     bam \\
         trimBam \\
         $bam \\
         ${prefix}.bam \\
-        $options.args \\
+        $args \\
         -L $trim_left \\
         -R $trim_right
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$( echo \$( bam trimBam 2>&1 ) | sed 's/^Version: //;s/;.*//' )
+        bamutil: \$( echo \$( bam trimBam 2>&1 ) | sed 's/^Version: //;s/;.*//' )
     END_VERSIONS
     """
 }

modules/bandage/image/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bandage/image/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BANDAGE_IMAGE {
     tag "${meta.id}"
     label 'process_low'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? 'bioconda::bandage=0.8.1' : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bandage:0.8.1--hc9558a2_2"
+        'https://depot.galaxyproject.org/singularity/bandage:0.8.1--hc9558a2_2' :
-    } else {
+        'quay.io/biocontainers/bandage:0.8.1--hc9558a2_2' }"
-        container "quay.io/biocontainers/bandage:0.8.1--hc9558a2_2"
-    }
 
     input:
     tuple val(meta), path(gfa)
@@ -27,14 +16,15 @@ process BANDAGE_IMAGE {
     path  "versions.yml"          , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     """
-    Bandage image $gfa ${prefix}.png $options.args
+    Bandage image $gfa ${prefix}.png $args
-    Bandage image $gfa ${prefix}.svg $options.args
+    Bandage image $gfa ${prefix}.svg $args
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(echo \$(Bandage --version 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+        bandage: \$(echo \$(Bandage --version 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/bbmap/align/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bbmap/align/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BBMAP_ALIGN {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.13 pigz=2.6" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0' :
-    } else {
+        'quay.io/biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0' }"
-        container "quay.io/biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0"
-    }
 
     input:
     tuple val(meta), path(fastq)
@@ -28,7 +17,8 @@ process BBMAP_ALIGN {
     path "versions.yml"           , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
 
     input = meta.single_end ? "in=${fastq}" : "in=${fastq[0]} in2=${fastq[1]}"
 
@@ -50,14 +40,14 @@ process BBMAP_ALIGN {
         $db \\
         $input \\
         out=${prefix}.bam \\
-        $options.args \\
+        $args \\
         threads=$task.cpus \\
         -Xmx${task.memory.toGiga()}g \\
         &> ${prefix}.bbmap.log
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(bbversion.sh)
+        bbmap: \$(bbversion.sh)
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
         pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
     END_VERSIONS

modules/bbmap/bbduk/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bbmap/bbduk/main.nf

@@ -1,21 +1,11 @@
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BBMAP_BBDUK {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bbmap=38.90" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bbmap:38.90--he522d1c_1"
+        'https://depot.galaxyproject.org/singularity/bbmap:38.90--he522d1c_1' :
-    } else {
+        'quay.io/biocontainers/bbmap:38.90--he522d1c_1' }"
-        container "quay.io/biocontainers/bbmap:38.90--he522d1c_1"
-    }
 
     input:
     tuple val(meta), path(reads)
@@ -27,7 +17,8 @@ process BBMAP_BBDUK {
     path "versions.yml"                , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     def raw      = meta.single_end ? "in=${reads[0]}" : "in1=${reads[0]} in2=${reads[1]}"
     def trimmed  = meta.single_end ? "out=${prefix}.fastq.gz" : "out1=${prefix}_1.fastq.gz out2=${prefix}_2.fastq.gz"
     def contaminants_fa = contaminants ? "ref=$contaminants" : ''
@@ -38,12 +29,12 @@ process BBMAP_BBDUK {
         $raw \\
         $trimmed \\
         threads=$task.cpus \\
-        $options.args \\
+        $args \\
         $contaminants_fa \\
         &> ${prefix}.bbduk.log
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(bbversion.sh)
+        bbmap: \$(bbversion.sh)
     END_VERSIONS
     """
 }

modules/bbmap/bbsplit/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bbmap/bbsplit/main.nf

@@ -1,21 +1,10 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BBMAP_BBSPLIT {
     label 'process_high'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bbmap=38.93" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bbmap:38.93--he522d1c_0"
+        'https://depot.galaxyproject.org/singularity/bbmap:38.93--he522d1c_0' :
-    } else {
+        'quay.io/biocontainers/bbmap:38.93--he522d1c_0' }"
-        container "quay.io/biocontainers/bbmap:38.93--he522d1c_0"
-    }
 
     input:
     tuple val(meta), path(reads)
@@ -32,7 +21,8 @@ process BBMAP_BBSPLIT {
     path "versions.yml"                       , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
 
     def avail_mem = 3
     if (!task.memory) {
@@ -54,11 +44,11 @@ process BBMAP_BBSPLIT {
                 ${other_refs.join(' ')} \\
                 path=bbsplit \\
                 threads=$task.cpus \\
-                $options.args
+                $args
 
             cat <<-END_VERSIONS > versions.yml
-            ${getProcessName(task.process)}:
+            "${task.process}":
-                ${getSoftwareName(task.process)}: \$(bbversion.sh 2>&1)
+                bbmap: \$(bbversion.sh 2>&1)
             END_VERSIONS
             """
         } else {
@@ -83,11 +73,11 @@ process BBMAP_BBSPLIT {
             $fastq_in \\
             $fastq_out \\
             refstats=${prefix}.stats.txt \\
-            $options.args
+            $args
 
         cat <<-END_VERSIONS > versions.yml
-        ${getProcessName(task.process)}:
+        "${task.process}":
-            ${getSoftwareName(task.process)}: \$(bbversion.sh 2>&1)
+            bbmap: \$(bbversion.sh 2>&1)
         END_VERSIONS
         """
     }

modules/bbmap/index/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bbmap/index/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BBMAP_INDEX {
     tag "$fasta"
     label 'process_long'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "bioconda::bbmap=38.92" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bbmap:38.92--he522d1c_0"
+        'https://depot.galaxyproject.org/singularity/bbmap:38.92--he522d1c_0' :
-    } else {
+        'quay.io/biocontainers/bbmap:38.92--he522d1c_0' }"
-        container "quay.io/biocontainers/bbmap:38.92--he522d1c_0"
-    }
 
     input:
     path fasta
@@ -26,16 +15,17 @@ process BBMAP_INDEX {
     path "versions.yml"           , emit: versions
 
     script:
+    def args = task.ext.args ?: ''
     """
     bbmap.sh \\
         ref=${fasta} \\
-        $options.args \\
+        $args \\
         threads=$task.cpus \\
         -Xmx${task.memory.toGiga()}g
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(bbversion.sh)
+        bbmap: \$(bbversion.sh)
     END_VERSIONS
     """
 }

modules/bcftools/concat/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bcftools/concat/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BCFTOOLS_CONCAT {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bcftools=1.11" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0' :
-    } else {
+        'quay.io/biocontainers/bcftools:1.11--h7c999a4_0' }"
-        container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
-    }
 
     input:
     tuple val(meta), path(vcfs)
@@ -26,17 +15,18 @@ process BCFTOOLS_CONCAT {
     path  "versions.yml"         , emit: versions
 
     script:
-    prefix       = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     """
     bcftools concat \\
         --output ${prefix}.vcf.gz \\
-        $options.args \\
+        $args \\
         --threads $task.cpus \\
         ${vcfs}
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/bcftools/consensus/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bcftools/consensus/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BCFTOOLS_CONSENSUS {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container 'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0'
+        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-    } else {
+        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
-        container 'quay.io/biocontainers/bcftools:1.13--h3a49de5_0'
-    }
 
     input:
     tuple val(meta), path(vcf), path(tbi), path(fasta)
@@ -26,15 +15,16 @@ process BCFTOOLS_CONSENSUS {
     path  "versions.yml"         , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     """
-    cat $fasta | bcftools consensus $vcf $options.args > ${prefix}.fa
+    cat $fasta | bcftools consensus $vcf $args > ${prefix}.fa
     header=\$(head -n 1 ${prefix}.fa | sed 's/>//g')
     sed -i 's/\${header}/${meta.id}/g' ${prefix}.fa
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/bcftools/filter/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bcftools/filter/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BCFTOOLS_FILTER {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-    } else {
+        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
-        container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
-    }
 
     input:
     tuple val(meta), path(vcf)
@@ -26,16 +15,17 @@ process BCFTOOLS_FILTER {
     path  "versions.yml"         , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     """
     bcftools filter \\
         --output ${prefix}.vcf.gz \\
-        $options.args \\
+        $args \\
         $vcf
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/bcftools/index/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bcftools/index/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BCFTOOLS_INDEX {
     tag "$meta.id"
     label 'process_low'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-    } else {
+        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
-        container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
-    }
 
     input:
     tuple val(meta), path(vcf)
@@ -27,18 +16,19 @@ process BCFTOOLS_INDEX {
     path "versions.yml"          , emit: version
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
 
     """
     bcftools \\
         index \\
-        $options.args \\
+        $args \\
         --threads $task.cpus \\
         $vcf
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/bcftools/isec/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bcftools/isec/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BCFTOOLS_ISEC {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-    } else {
+        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
-        container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
-    }
 
     input:
     tuple val(meta), path(vcfs), path(tbis)
@@ -26,15 +15,16 @@ process BCFTOOLS_ISEC {
     path  "versions.yml"              , emit: versions
 
     script:
-    prefix       = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     """
     bcftools isec  \\
-        $options.args \\
+        $args \\
         -p $prefix \\
         *.vcf.gz
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/bcftools/merge/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bcftools/merge/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BCFTOOLS_MERGE {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-    } else {
+        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
-        container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
-    }
 
     input:
     tuple val(meta), path(vcfs), path(tbis)
@@ -26,15 +15,16 @@ process BCFTOOLS_MERGE {
     path  "versions.yml"         , emit: versions
 
     script:
-    prefix       = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     """
     bcftools merge -Oz \\
         --output ${prefix}.vcf.gz \\
-        $options.args \\
+        $args \\
         *.vcf.gz
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/bcftools/mpileup/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bcftools/mpileup/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BCFTOOLS_MPILEUP {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-    } else {
+        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
-        container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
-    }
 
     input:
     tuple val(meta), path(bam)
@@ -29,21 +18,28 @@ process BCFTOOLS_MPILEUP {
     path  "versions.yml"               , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def args3 = task.ext.args3 ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     """
     echo "${meta.id}" > sample_name.list
+
     bcftools mpileup \\
         --fasta-ref $fasta \\
-        $options.args \\
+        $args \\
         $bam \\
-        | bcftools call --output-type v $options.args2 \\
+        | bcftools call --output-type v $args2 \\
         | bcftools reheader --samples sample_name.list \\
-        | bcftools view --output-file ${prefix}.vcf.gz --output-type z $options.args3
+        | bcftools view --output-file ${prefix}.vcf.gz --output-type z $args3
+
     tabix -p vcf -f ${prefix}.vcf.gz
+
     bcftools stats ${prefix}.vcf.gz > ${prefix}.bcftools_stats.txt
+
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/bcftools/norm/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bcftools/norm/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BCFTOOLS_NORM {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bcftools=1.13" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-    } else {
+        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
-        container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
-    }
 
     input:
     tuple val(meta), path(vcf)
@@ -27,18 +16,19 @@ process BCFTOOLS_NORM {
     path "versions.yml"           , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     """
     bcftools norm \\
         --fasta-ref ${fasta} \\
         --output ${prefix}.vcf.gz \\
-        $options.args \\
+        $args \\
         --threads $task.cpus \\
         ${vcf}
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/bcftools/query/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bcftools/query/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BCFTOOLS_QUERY {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bcftools=1.13" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-    } else {
+        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
-        container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
-    }
 
     input:
     tuple val(meta), path(vcf), path(index)
@@ -29,7 +18,8 @@ process BCFTOOLS_QUERY {
     path "versions.yml"           , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     def regions_file  = regions ? "--regions-file ${regions}" : ""
     def targets_file = targets ? "--targets-file ${targets}" : ""
     def samples_file =  samples ? "--samples-file ${samples}" : ""
@@ -40,12 +30,12 @@ process BCFTOOLS_QUERY {
         ${regions_file} \\
         ${targets_file} \\
         ${samples_file} \\
-        $options.args \\
+        $args \\
         ${vcf}
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/bcftools/reheader/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bcftools/reheader/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BCFTOOLS_REHEADER {
     tag "$meta.id"
     label 'process_low'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bcftools=1.13" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-    } else {
+        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
-        container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
-    }
 
     input:
     tuple val(meta), path(vcf)
@@ -28,7 +17,8 @@ process BCFTOOLS_REHEADER {
     path "versions.yml"              , emit: versions
 
     script:
-    def prefix           = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     def update_sequences = fai ? "-f $fai" : ""
     def new_header       = header ? "-h $header" : ""
     """
@@ -36,14 +26,14 @@ process BCFTOOLS_REHEADER {
         reheader \\
         $update_sequences \\
         $new_header \\
-        $options.args \\
+        $args \\
         --threads $task.cpus \\
         -o ${prefix}.vcf.gz \\
         $vcf
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/bcftools/stats/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bcftools/stats/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BCFTOOLS_STATS {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-    } else {
+        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
-        container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
-    }
 
     input:
     tuple val(meta), path(vcf)
@@ -26,12 +15,13 @@ process BCFTOOLS_STATS {
     path  "versions.yml"               , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     """
-    bcftools stats $options.args $vcf > ${prefix}.bcftools_stats.txt
+    bcftools stats $args $vcf > ${prefix}.bcftools_stats.txt
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/bcftools/view/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bcftools/view/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BCFTOOLS_VIEW {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bcftools=1.13" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-    } else {
+        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
-        container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
-    }
 
     input:
     tuple val(meta), path(vcf), path(index)
@@ -29,25 +18,24 @@ process BCFTOOLS_VIEW {
     path "versions.yml"           , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     def regions_file  = regions ? "--regions-file ${regions}" : ""
     def targets_file = targets ? "--targets-file ${targets}" : ""
     def samples_file =  samples ? "--samples-file ${samples}" : ""
-
-
     """
     bcftools view \\
         --output ${prefix}.vcf.gz \\
         ${regions_file} \\
         ${targets_file} \\
         ${samples_file} \\
-        $options.args \\
+        $args \\
         --threads $task.cpus \\
         ${vcf}
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/bedtools/bamtobed/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bedtools/bamtobed/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BEDTOOLS_BAMTOBED {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
+        'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
-    } else {
+        'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
-        container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
-    }
 
     input:
     tuple val(meta), path(bam)
@@ -26,17 +15,18 @@ process BEDTOOLS_BAMTOBED {
     path  "versions.yml"          , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     """
     bedtools \\
         bamtobed \\
-        $options.args \\
+        $args \\
         -i $bam \\
         | bedtools sort > ${prefix}.bed
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
     END_VERSIONS
     """
 }

modules/bedtools/complement/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bedtools/complement/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BEDTOOLS_COMPLEMENT {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
+        'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
-    } else {
+        'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
-        container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
-    }
 
     input:
     tuple val(meta), path(bed)
@@ -27,18 +16,19 @@ process BEDTOOLS_COMPLEMENT {
     path  "versions.yml"          , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     """
     bedtools \\
         complement \\
         -i $bed \\
         -g $sizes \\
-        $options.args \\
+        $args \\
         > ${prefix}.bed
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
     END_VERSIONS
     """
 }

modules/bedtools/genomecov/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bedtools/genomecov/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BEDTOOLS_GENOMECOV {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
+        'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
-    } else {
+        'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
-        container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
-    }
 
     input:
     tuple val(meta), path(intervals), val(scale)
@@ -28,15 +17,14 @@ process BEDTOOLS_GENOMECOV {
     path  "versions.yml"                   , emit: versions
 
     script:
-    def prefix     = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
-    def args_token = options.args.tokenize()
+    def args_list = args.tokenize()
-    def args       = options.args
     args += (scale > 0 && scale != 1) ? " -scale $scale" : ""
-
+    if (!args_list.contains('-bg') && (scale > 0 && scale != 1)) {
-    if (!args_token.contains('-bg') && (scale > 0 && scale != 1)) {
         args += " -bg"
     }
 
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     if (intervals.name =~ /\.bam/) {
         """
         bedtools \\
@@ -46,8 +34,8 @@ process BEDTOOLS_GENOMECOV {
             > ${prefix}.${extension}
 
         cat <<-END_VERSIONS > versions.yml
-        ${getProcessName(task.process)}:
+        "${task.process}":
-            ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+            bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
         END_VERSIONS
         """
     } else {
@@ -60,8 +48,8 @@ process BEDTOOLS_GENOMECOV {
             > ${prefix}.${extension}
 
         cat <<-END_VERSIONS > versions.yml
-        ${getProcessName(task.process)}:
+        "${task.process}":
-            ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+            bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
         END_VERSIONS
         """
     }

modules/bedtools/getfasta/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bedtools/getfasta/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BEDTOOLS_GETFASTA {
     tag "$bed"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
+        'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
-    } else {
+        'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
-        container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
-    }
 
     input:
     path bed
@@ -27,18 +16,19 @@ process BEDTOOLS_GETFASTA {
     path "versions.yml" , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${bed.baseName}${options.suffix}" : "${bed.baseName}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${bed.baseName}${task.ext.suffix}" : "${bed.baseName}"
     """
     bedtools \\
         getfasta \\
-        $options.args \\
+        $args \\
         -fi $fasta \\
         -bed $bed \\
         -fo ${prefix}.fa
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
     END_VERSIONS
     """
 }

modules/bedtools/intersect/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bedtools/intersect/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BEDTOOLS_INTERSECT {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
+        'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
-    } else {
+        'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
-        container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
-    }
 
     input:
     tuple val(meta), path(intervals1), path(intervals2)
@@ -27,18 +16,19 @@ process BEDTOOLS_INTERSECT {
     path  "versions.yml"                   , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     """
     bedtools \\
         intersect \\
         -a $intervals1 \\
         -b $intervals2 \\
-        $options.args \\
+        $args \\
         > ${prefix}.${extension}
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
     END_VERSIONS
     """
 }

modules/bedtools/makewindows/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bedtools/makewindows/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BEDTOOLS_MAKEWINDOWS {
     tag "$meta.id"
     label 'process_low'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--h7d7f7ad_1"
+        'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--h7d7f7ad_1' :
-    } else {
+        'quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_1' }"
-        container "quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_1"
-    }
 
     input:
     tuple val(meta), path(regions)
@@ -27,18 +16,19 @@ process BEDTOOLS_MAKEWINDOWS {
     path "versions.yml"           , emit: versions
 
     script:
-    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     def arg_input = use_bed ? "-b $regions" : "-g $regions"
     """
     bedtools \\
         makewindows \\
         ${arg_input} \\
-        $options.args \\
+        $args \\
         > ${prefix}.tab
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
     END_VERSIONS
     """
 }

modules/bedtools/maskfasta/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bedtools/maskfasta/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BEDTOOLS_MASKFASTA {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
+        'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
-    } else {
+        'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
-        container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
-    }
 
     input:
     tuple val(meta), path(bed)
@@ -27,17 +16,18 @@ process BEDTOOLS_MASKFASTA {
     path "versions.yml"          , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     """
     bedtools \\
         maskfasta \\
-        $options.args \\
+        $args \\
         -fi $fasta \\
         -bed $bed \\
         -fo ${prefix}.fa
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
     END_VERSIONS
     """
 }

modules/bedtools/merge/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bedtools/merge/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BEDTOOLS_MERGE {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
+        'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
-    } else {
+        'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
-        container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
-    }
 
     input:
     tuple val(meta), path(bed)
@@ -26,17 +15,18 @@ process BEDTOOLS_MERGE {
     path  "versions.yml"          , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     """
     bedtools \\
         merge \\
         -i $bed \\
-        $options.args \\
+        $args \\
         > ${prefix}.bed
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
     END_VERSIONS
     """
 }

modules/bedtools/slop/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bedtools/slop/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BEDTOOLS_SLOP {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
+        'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
-    } else {
+        'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
-        container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
-    }
 
     input:
     tuple val(meta), path(bed)
@@ -27,18 +16,19 @@ process BEDTOOLS_SLOP {
     path  "versions.yml"          , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     """
     bedtools \\
         slop \\
         -i $bed \\
         -g $sizes \\
-        $options.args \\
+        $args \\
         > ${prefix}.bed
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
     END_VERSIONS
     """
 

modules/bedtools/sort/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bedtools/sort/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BEDTOOLS_SORT {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
+        'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
-    } else {
+        'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
-        container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
-    }
 
     input:
     tuple val(meta), path(intervals)
@@ -27,17 +16,18 @@ process BEDTOOLS_SORT {
     path  "versions.yml"                   , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     """
     bedtools \\
         sort \\
         -i $intervals \\
-        $options.args \\
+        $args \\
         > ${prefix}.${extension}
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
     END_VERSIONS
     """
 }

modules/bedtools/subtract/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bedtools/subtract/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BEDTOOLS_SUBTRACT {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
+        'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
-    } else {
+        'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
-        container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
-    }
 
     input:
     tuple val(meta), path(intervals1), path(intervals2)
@@ -26,18 +15,19 @@ process BEDTOOLS_SUBTRACT {
     path "versions.yml"           , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     """
     bedtools \\
         subtract \\
         -a $intervals1 \\
         -b $intervals2 \\
-        $options.args \\
+        $args \\
         > ${prefix}.bed
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
     END_VERSIONS
     """
 }

modules/bismark/align/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bismark/align/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options    = initOptions(params.options)
-
 process BISMARK_ALIGN {
     tag "$meta.id"
     label 'process_high'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bismark:0.23.0--0"
+        'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' :
-    } else {
+        'quay.io/biocontainers/bismark:0.23.0--0' }"
-        container "quay.io/biocontainers/bismark:0.23.0--0"
-    }
 
     input:
     tuple val(meta), path(reads)
@@ -29,18 +18,19 @@ process BISMARK_ALIGN {
     path "versions.yml"                 , emit: versions
 
     script:
-    def prefix     = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     def fastq      = meta.single_end ? reads : "-1 ${reads[0]} -2 ${reads[1]}"
     """
     bismark \\
         $fastq \\
-        $options.args \\
+        $args \\
         --genome $index \\
         --bam
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
+        bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
     END_VERSIONS
     """
 }

modules/bismark/deduplicate/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bismark/deduplicate/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BISMARK_DEDUPLICATE {
     tag "$meta.id"
     label 'process_high'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bismark:0.23.0--0"
+        'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' :
-    } else {
+        'quay.io/biocontainers/bismark:0.23.0--0' }"
-        container "quay.io/biocontainers/bismark:0.23.0--0"
-    }
 
     input:
     tuple val(meta), path(bam)
@@ -27,17 +16,18 @@ process BISMARK_DEDUPLICATE {
     path  "versions.yml"                               , emit: versions
 
     script:
-    def prefix     = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     def seqtype    = meta.single_end ? '-s' : '-p'
     """
     deduplicate_bismark \\
-        $options.args \\
+        $args \\
         $seqtype \\
         --bam $bam
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
+        bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
     END_VERSIONS
     """
 }

modules/bismark/genomepreparation/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bismark/genomepreparation/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BISMARK_GENOMEPREPARATION {
     tag "$fasta"
     label 'process_high'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bismark:0.23.0--0"
+        'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' :
-    } else {
+        'quay.io/biocontainers/bismark:0.23.0--0' }"
-        container "quay.io/biocontainers/bismark:0.23.0--0"
-    }
 
     input:
     path fasta, stageAs: "BismarkIndex/*"
@@ -26,14 +15,15 @@ process BISMARK_GENOMEPREPARATION {
     path "versions.yml" , emit: versions
 
     script:
+    def args = task.ext.args ?: ''
     """
     bismark_genome_preparation \\
-        $options.args \\
+        $args \\
         BismarkIndex
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
+        bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
     END_VERSIONS
     """
 }

modules/bismark/methylationextractor/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bismark/methylationextractor/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BISMARK_METHYLATIONEXTRACTOR {
     tag "$meta.id"
     label 'process_high'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bismark:0.23.0--0"
+        'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' :
-    } else {
+        'quay.io/biocontainers/bismark:0.23.0--0' }"
-        container "quay.io/biocontainers/bismark:0.23.0--0"
-    }
 
     input:
     tuple val(meta), path(bam)
@@ -31,6 +20,7 @@ process BISMARK_METHYLATIONEXTRACTOR {
     path "versions.yml"                            , emit: versions
 
     script:
+    def args = task.ext.args ?: ''
     def seqtype  = meta.single_end ? '-s' : '-p'
     """
     bismark_methylation_extractor \\
@@ -39,12 +29,12 @@ process BISMARK_METHYLATIONEXTRACTOR {
         --gzip \\
         --report \\
         $seqtype \\
-        $options.args \\
+        $args \\
         $bam
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
+        bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
     END_VERSIONS
     """
 }

modules/bismark/report/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bismark/report/main.nf

@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BISMARK_REPORT {
     tag "$meta.id"
     label 'process_low'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bismark:0.23.0--0"
+        'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' :
-    } else {
+        'quay.io/biocontainers/bismark:0.23.0--0' }"
-        container "quay.io/biocontainers/bismark:0.23.0--0"
-    }
 
     input:
     tuple val(meta), path(align_report), path(dedup_report), path(splitting_report), path(mbias)
@@ -26,12 +15,13 @@ process BISMARK_REPORT {
     path  "versions.yml"                       , emit: versions
 
     script:
+    def args = task.ext.args ?: ''
     """
-    bismark2report $options.args
+    bismark2report $args
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
+        bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
     END_VERSIONS
     """
 }

modules/bismark/summary/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}

modules/bismark/summary/main.nf

@@ -1,21 +1,10 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BISMARK_SUMMARY {
     label 'process_low'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        container "https://depot.galaxyproject.org/singularity/bismark:0.23.0--0"
+        'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' :
-    } else {
+        'quay.io/biocontainers/bismark:0.23.0--0' }"
-        container "quay.io/biocontainers/bismark:0.23.0--0"
-    }
 
     input:
     path(bam)
@@ -29,12 +18,13 @@ process BISMARK_SUMMARY {
     path  "versions.yml"      , emit: versions
 
     script:
+    def args = task.ext.args ?: ''
     """
     bismark2summary
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    "${task.process}":
-        ${getSoftwareName(task.process)}: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
+        bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
     END_VERSIONS
     """
 }

modules/blast/blastn/functions.nf

@@ -1,78 +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()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}