Merge branch 'nf-core:master' into master

.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

@@ -6,11 +6,8 @@ on:
     branches: [master]
 
 jobs:
-  ###########
+  changes:
-  # Modules #
+    name: Check for changes
-  ###########
-  module_changes:
-    name: Check for changes in the modules
     runs-on: ubuntu-latest
     outputs:
       # Expose matched filters as job 'modules' output variable
@@ -23,17 +20,16 @@ jobs:
         with:
           filters: "tests/config/pytest_modules.yml"
 
-  module_test:
+  test:
     runs-on: ubuntu-20.04
 
-    name: ${{ matrix.tags }} ${{ matrix.profile }} ${{ matrix.nxf_version }}
+    name: ${{ matrix.tags }} ${{ matrix.profile }}
-    needs: module_changes
+    needs: changes
-    if: needs.module_changes.outputs.modules != '[]'
+    if: needs.changes.outputs.modules != '[]'
     strategy:
       fail-fast: false
       matrix:
-        nxf_version: ["21.04.0"]
+        tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
-        tags: ${{ fromJson(needs.module_changes.outputs.modules) }}
         profile: ["docker", "singularity", "conda"]
     env:
       NXF_ANSI_LOG: false
@@ -63,13 +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: ${{ matrix.nxf_version }}
           CAPSULE_LOG: none
         run: |
           wget -qO- get.nextflow.io | bash
@@ -96,118 +91,17 @@ jobs:
       # Test the module
       - name: Run pytest-workflow
         # only use one thread for pytest-workflow to avoid race condition on conda cache.
-        run: NF_CORE_MODULES_TEST=1 TMPDIR=~ PROFILE=${{ 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
-            /home/runner/pytest_workflow_*/*/log.err
-            /home/runner/pytest_workflow_*/*/work
-
-  ################
-  # Subworkflows #
-  ################
-  subworkflow_changes:
-    name: Check for changes in the subworkflows
-    runs-on: ubuntu-latest
-    outputs:
-      # Expose matched filters as job 'subworkflows' output variable
-      subworkflows: ${{ steps.filter.outputs.changes }}
-    steps:
-      - uses: actions/checkout@v2
-
-      - uses: dorny/paths-filter@v2
-        id: filter
-        with:
-          filters: "tests/config/pytest_subworkflows.yml"
-
-  subworkflow_test:
-    runs-on: ubuntu-20.04
-
-    name: ${{ matrix.tags }} ${{ matrix.profile }} ${{ matrix.nxf_version }}
-    needs: subworkflow_changes
-    if: needs.subworkflow_changes.outputs.subworkflows != '[]'
-    strategy:
-      fail-fast: false
-      matrix:
-        nxf_version: ["21.04.0"]
-        tags: ${{ fromJson(needs.subworkflow_changes.outputs.subworkflows) }}
-        profile: ["docker", "singularity", "conda"]
-    env:
-      NXF_ANSI_LOG: false
-    steps:
-      - uses: actions/checkout@v2
-
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: "3.x"
-
-      - uses: actions/cache@v2
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
-
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: "3.x"
-
-      - name: Install Python dependencies
-        run: python -m pip install --upgrade pip pytest-workflow
-
-      - uses: actions/cache@v2
-        with:
-          path: /usr/local/bin/nextflow
-          key: ${{ runner.os }}-nextflow-${{ matrix.nxf_version }}
-          restore-keys: |
-            ${{ runner.os }}-nextflow-
-
-      - name: Install Nextflow
-        env:
-          NXF_VER: ${{ matrix.nxf_version }}
-          CAPSULE_LOG: none
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Set up Singularity
-        if: matrix.profile == 'singularity'
-        uses: eWaterCycle/setup-singularity@v5
-        with:
-          singularity-version: 3.7.1
-
-      - name: Setup miniconda
-        if: matrix.profile == 'conda'
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          channels: conda-forge,bioconda,defaults
-          python-version: ${{ matrix.python-version }}
-
-      - name: Conda clean
-        if: matrix.profile == 'conda'
-        run: conda clean -a
-
-      # Test the module
-      - name: Run pytest-workflow
-        # only use one thread for pytest-workflow to avoid race condition on conda cache.
-        run: NF_CORE_MODULES_TEST=1 TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof
-
-      - name: Upload logs on failure
-        if: failure()
-        uses: actions/upload-artifact@v2
-        with:
-          name: logs-${{ matrix.profile }}-${{ matrix.nxf_version }}
           path: |
             /home/runner/pytest_workflow_*/*/.nextflow.log
             /home/runner/pytest_workflow_*/*/log.out
             /home/runner/pytest_workflow_*/*/log.err
             /home/runner/pytest_workflow_*/*/work
+            !/home/runner/pytest_workflow_*/*/work/conda
+            !/home/runner/pytest_workflow_*/*/work/singularity

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:

main.nf

@@ -0,0 +1,3 @@
+/*
+ * not actually used - just a placeholder
+ */

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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
 
     if (meta.single_end) {
         """
         AdapterRemoval  \\
             --file1 $reads \\
-            $options.args \\
+            $args \\
             --basename $prefix \\
             --threads $task.cpus \\
             --settings ${prefix}.log \\
@@ -41,16 +32,16 @@ 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) {
         """
         AdapterRemoval  \\
             --file1 ${reads[0]} \\
-            --file2 ${reads[0]} \\
+            --file2 ${reads[1]} \\
-            $options.args \\
+            $args \\
             --basename $prefix \\
             --threads $task.cpus \\
             --settings ${prefix}.log \\
@@ -60,17 +51,17 @@ 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 {
         """
         AdapterRemoval  \\
             --file1 ${reads[0]} \\
-            --file2 ${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=1.0.1" : null)
+    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:1.0.1--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:1.0.1--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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
-    def blacklist = (options.args.contains('-b')) ? '' : '-f blacklist'
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args   ?: ''
+    prefix   = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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/main.nf

@@ -0,0 +1,47 @@
+process ATAQV_ATAQV {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::ataqv=1.2.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ataqv:1.2.1--py39ha23c084_2' :
+        'quay.io/biocontainers/ataqv:1.2.1--py36hfdecbe1_2' }"
+
+    input:
+    tuple val(meta), path(bam), path(bai), path(peak_file)
+    val organism
+    path tss_file
+    path excl_regs_file
+    path autosom_ref_file
+
+    output:
+    tuple val(meta), path("*.ataqv.json"), emit: json
+    tuple val(meta), path("*.problems")  , emit: problems, optional: true
+    path "versions.yml"                  , emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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 \\
+        $args \\
+        $peak \\
+        $tss \\
+        $excl_regs \\
+        $autosom_ref \\
+        --metrics-file "${prefix}.ataqv.json" \\
+        --threads $task.cpus \\
+        --name $prefix \\
+        $organism \\
+        $bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ataqv: \$( ataqv --version )
+    END_VERSIONS
+    """
+}

modules/ataqv/ataqv/meta.yml

@@ -0,0 +1,66 @@
+name: ataqv_ataqv
+description: ataqv function of a corresponding ataqv tool
+keywords:
+  - ataqv
+tools:
+  - ataqv:
+      description: ataqv is a toolkit for measuring and comparing ATAC-seq results. It was written to help understand how well ATAC-seq assays have worked, and to make it easier to spot differences that might be caused by library prep or sequencing.
+      homepage: https://github.com/ParkerLab/ataqv/blob/master/README.rst
+      documentation: https://github.com/ParkerLab/ataqv/blob/master/README.rst
+      tool_dev_url: https://github.com/ParkerLab/ataqv
+      doi: "https://doi.org/10.1016/j.cels.2020.02.009"
+      licence: ['GPL v3']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM file
+      pattern: "*.bam"
+  - bai:
+      type: file
+      description: BAM index file with the same prefix as bam file. Required if tss_file input is provided.
+      pattern: "*.bam.bai"
+  - peak_file:
+      type: file
+      description: A BED file of peaks called for alignments in the BAM file
+      pattern: "*.bed"
+  - organism:
+      type: string
+      description: The subject of the experiment, which determines the list of autosomes (see "Reference Genome Configuration" section at https://github.com/ParkerLab/ataqv).
+  - tss_file:
+      type: file
+      description: A BED file of transcription start sites for the experiment organism. If supplied, a TSS enrichment score will be calculated according to the ENCODE data standards. This calculation requires that the BAM file of alignments be indexed.
+      pattern: "*.bed"
+  - excl_regs_file:
+      type: file
+      description: A BED file containing excluded regions. Peaks or TSS overlapping these will be ignored.
+      pattern: "*.bed"
+  - autosom_ref_file:
+      type: file
+      description: A file containing autosomal reference names, one per line. The names must match the reference names in the alignment file exactly, or the metrics based on counts of autosomal alignments will be wrong.
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - json:
+      type: file
+      description: The JSON file to which metrics will be written.
+  - problems:
+      type: file
+      description: If given, problematic reads will be logged to a file per read group, with names derived from the read group IDs, with ".problems" appended. If no read groups are found, the reads will be written to one file named after the BAM file.
+      pattern: "*.problems"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@i-pletenev"

modules/bakta/main.nf

@@ -0,0 +1,67 @@
+process BAKTA {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::bakta=1.2.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bakta:1.2.2--pyhdfd78af_0' :
+        'quay.io/biocontainers/bakta:1.2.2--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+    path db
+    path proteins
+    path prodigal_tf
+
+    output:
+    tuple val(meta), path("${prefix}.embl")             , emit: embl
+    tuple val(meta), path("${prefix}.faa")              , emit: faa
+    tuple val(meta), path("${prefix}.ffn")              , emit: ffn
+    tuple val(meta), path("${prefix}.fna")              , emit: fna
+    tuple val(meta), path("${prefix}.gbff")             , emit: gbff
+    tuple val(meta), path("${prefix}.gff3")             , emit: gff
+    tuple val(meta), path("${prefix}.hypotheticals.tsv"), emit: hypotheticals_tsv
+    tuple val(meta), path("${prefix}.hypotheticals.faa"), emit: hypotheticals_faa
+    tuple val(meta), path("${prefix}.tsv")              , emit: tsv
+    path "versions.yml"                                 , emit: versions
+
+    script:
+    def args = task.ext.args   ?: ''
+    prefix   = task.ext.prefix ?: "${meta.id}"
+    def proteins_opt = proteins ? "--proteins ${proteins[0]}" : ""
+    def prodigal_opt = prodigal_tf ? "--prodigal-tf ${prodigal_tf[0]}" : ""
+    """
+    bakta \\
+        $args \\
+        --threads $task.cpus \\
+        --prefix $prefix \\
+        --db $db \\
+        $proteins_opt \\
+        $prodigal_tf \\
+        $fasta
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bakta: \$( echo \$(bakta --version 2>&1) | sed 's/^.*bakta //' )
+    END_VERSIONS
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.embl
+    touch ${prefix}.faa
+    touch ${prefix}.ffn
+    touch ${prefix}.fna
+    touch ${prefix}.gbff
+    touch ${prefix}.gff3
+    touch ${prefix}.hypotheticals.tsv
+    touch ${prefix}.hypotheticals.faa
+    touch ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bakta: \$( echo \$(bakta --version 2>&1) | sed 's/^.*bakta //' )
+    END_VERSIONS
+    """
+}

modules/bakta/meta.yml

@@ -0,0 +1,85 @@
+name: bakta
+description: Rapid annotation of bacterial genomes & plasmids.
+keywords:
+  - annotation
+  - fasta
+  - prokaryote
+tools:
+  - bakta:
+      description: Rapid & standardized annotation of bacterial genomes & plasmids.
+      homepage: https://github.com/oschwengers/bakta
+      documentation: https://github.com/oschwengers/bakta
+      tool_dev_url: https://github.com/oschwengers/bakta
+      doi: "10.1099/mgen.0.000685"
+      licence: ['GPL v3']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: |
+        FASTA file to be annotated. Has to contain at least a non-empty string dummy value.
+  - db:
+      type: file
+      description: |
+        Path to the Bakta database
+  - proteins:
+      type: file
+      description: FASTA file of trusted proteins to first annotate from (optional)
+  - prodigal_tf:
+      type: file
+      description: Training file to use for Prodigal (optional)
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - tsv:
+      type: file
+      description: annotations as simple human readble tab separated values
+      pattern: "*.tsv"
+  - gff:
+      type: file
+      description: annotations & sequences in GFF3 format
+      pattern: "*.gff3"
+  - gbff:
+      type: file
+      description: annotations & sequences in (multi) GenBank format
+      pattern: "*.gbff"
+  - embl:
+      type: file
+      description: annotations & sequences in (multi) EMBL format
+      pattern: "*.embl"
+  - fna:
+      type: file
+      description: replicon/contig DNA sequences as FASTA
+      pattern: "*.fna"
+  - faa:
+      type: file
+      description: CDS/sORF amino acid sequences as FASTA
+      pattern: "*.faa"
+  - ffn:
+      type: file
+      description: feature nucleotide sequences as FASTA
+      pattern: "*.ffn"
+  - hypotheticals_tsv:
+      type: file
+      description: further information on hypothetical protein CDS as simple human readble tab separated values
+      pattern: "*.hypotheticals.tsv"
+  - hypotheticals_faa:
+      type: file
+      description: hypothetical protein CDS amino acid sequences as FASTA
+      pattern: "*.hypotheticals.faa"
+
+authors:
+  - "@rpetit3"

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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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/main.nf

@@ -0,0 +1,34 @@
+process BAMUTIL_TRIMBAM {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::bamutil=1.0.15" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bamutil:1.0.15--h2e03b76_1' :
+        'quay.io/biocontainers/bamutil:1.0.15--h2e03b76_1' }"
+
+    input:
+    tuple val(meta), path(bam), val(trim_left), val(trim_right)
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    path "versions.yml"           , emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    bam \\
+        trimBam \\
+        $bam \\
+        ${prefix}.bam \\
+        $args \\
+        -L $trim_left \\
+        -R $trim_right
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bamutil: \$( echo \$( bam trimBam 2>&1 ) | sed 's/^Version: //;s/;.*//' )
+    END_VERSIONS
+    """
+}

modules/bamutil/trimbam/meta.yml

@@ -0,0 +1,51 @@
+name: bamutil_trimbam
+description: trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’, or by soft clipping
+keywords:
+  - bam
+  - trim
+  - clipping
+  - bamUtil
+  - trimBam
+tools:
+  - bamutil:
+      description: Programs that perform operations on SAM/BAM files, all built into a single executable, bam.
+      homepage: https://genome.sph.umich.edu/wiki/BamUtil
+      documentation: https://genome.sph.umich.edu/wiki/BamUtil:_trimBam
+      tool_dev_url: https://github.com/statgen/bamUtil
+      doi: "10.1101/gr.176552.114"
+      licence: ['GPL v3']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM file
+      pattern: "*.bam"
+  - trim_left:
+      type: integer
+      description: Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming.
+  - trim_right:
+      type: integer
+      description: Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming.
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - bam:
+      type: file
+      description: Trimmed but unsorted BAM file
+      pattern: "*.bam"
+
+authors:
+  - "@jfy133"

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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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)
@@ -24,10 +13,12 @@ process BBMAP_ALIGN {
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
+    tuple val(meta), path("*.log"), emit: log
     path "versions.yml"           , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
 
     input = meta.single_end ? "in=${fastq}" : "in=${fastq[0]} in2=${fastq[1]}"
 
@@ -49,13 +40,14 @@ process BBMAP_ALIGN {
         $db \\
         $input \\
         out=${prefix}.bam \\
-        $options.args \\
+        $args \\
         threads=$task.cpus \\
-        -Xmx${task.memory.toGiga()}g
+        -Xmx${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args   ?: ''
+    prefix   = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args   ?: ''
+    prefix   = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args   ?: ''
+    prefix   = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def args3 = task.ext.args3 ?: ''
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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.prefix ?: "${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}" : "${bed.baseName}"
+    def args   = task.ext.args   ?: ''
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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
     """
 }