Merge remote-tracking branch 'nf-core/master'

.github/PULL_REQUEST_TEMPLATE.md

@@ -20,7 +20,7 @@ Closes #XXX <!-- If this PR fixes an issue, please link it here! -->
 - [ ] If you've added a new tool - have you followed the module conventions in the [contribution docs](https://github.com/nf-core/modules/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, include test data in your PR.
 - [ ] Remove all TODO statements.
-- [ ] Emit the `<SOFTWARE>.version.txt` file.
+- [ ] Emit the `versions.yml` file.
 - [ ] Follow the naming conventions.
 - [ ] Follow the parameters requirements.
 - [ ] Follow the input/output options guidelines.

.github/workflows/code-linting.yml

@@ -1,5 +1,10 @@
 name: Code Linting
-on: [push, pull_request]
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
 
 jobs:
   Markdown:

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

@@ -1,7 +1,12 @@
 name: nf-core linting
 # This workflow is triggered on pushes and PRs to the repository.
 # It runs the `nf-core lint` tests to ensure that the module code meets the nf-core guidelines
-on: [push, pull_request]
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
 
 jobs:
   changes:
@@ -66,6 +71,8 @@ jobs:
 
       - name: Lint ${{ matrix.tags }}
         run: nf-core modules lint ${{ matrix.tags }}
+        # HACK
+        if: startsWith( matrix.tags, 'subworkflow' ) != true
 
       - uses: actions/cache@v2
         with:

.github/workflows/pytest-workflow.yml

@@ -1,9 +1,16 @@
 name: Pytest-workflow
-on: [push, pull_request]
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
 
 jobs:
-  changes:
+  ###########
-    name: Check for changes
+  # Modules #
+  ###########
+  module_changes:
+    name: Check for changes in the modules
     runs-on: ubuntu-latest
     outputs:
       # Expose matched filters as job 'modules' output variable
@@ -16,17 +23,17 @@ jobs:
         with:
           filters: "tests/config/pytest_modules.yml"
 
-  test:
+  module_test:
     runs-on: ubuntu-20.04
 
     name: ${{ matrix.tags }} ${{ matrix.profile }} ${{ matrix.nxf_version }}
-    needs: changes
+    needs: module_changes
-    if: needs.changes.outputs.modules != '[]'
+    if: needs.module_changes.outputs.modules != '[]'
     strategy:
       fail-fast: false
       matrix:
         nxf_version: ["21.04.0"]
-        tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
+        tags: ${{ fromJson(needs.module_changes.outputs.modules) }}
         profile: ["docker", "singularity", "conda"]
     env:
       NXF_ANSI_LOG: false
@@ -89,7 +96,110 @@ jobs:
       # Test the module
       - name: Run pytest-workflow
         # only use one thread for pytest-workflow to avoid race condition on conda cache.
-        run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof
+        run: NF_CORE_MODULES_TEST=1 TMPDIR=~ PROFILE=${{ 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
+
+  ################
+  # 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()

.gitignore

@@ -5,6 +5,9 @@ test_output/
 output/
 .DS_Store
 *.code-workspace
+tests/data/
 .screenrc
 .*.sw?
-tests/data/
+__pycache__
+*.pyo
+*.pyc

modules/abacas/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/abacas/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -24,10 +24,9 @@ process ABACAS {
 
     output:
     tuple val(meta), path('*.abacas*'), emit: results
-    path '*.version.txt'              , emit: version
+    path "versions.yml"               , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     abacas.pl \\
@@ -40,6 +39,9 @@ process ABACAS {
     mv nucmer.filtered.delta ${prefix}.abacas.nucmer.filtered.delta
     mv nucmer.tiling ${prefix}.abacas.nucmer.tiling
     mv unused_contigs.out ${prefix}.abacas.unused.contigs.out
-    echo \$(abacas.pl -v 2>&1) | sed 's/^.*ABACAS.//; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo \$(abacas.pl -v 2>&1) | sed 's/^.*ABACAS.//; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/abacas/meta.yml

@@ -48,10 +48,10 @@ output:
         'test.abacas.MULTIFASTA.fa' ]
       pattern: "*.{abacas}*"
 
-  - version:
+  - versions:
       type: file
-      description: File containing software version
+      description: File containing software versions
-      pattern: "*.{version.txt}"
+      pattern: "versions.yml"
 
 authors:
   - "@joseespinosa"

modules/adapterremoval/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/adapterremoval/main.nf

@@ -1,4 +1,4 @@
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,10 +23,9 @@ process ADAPTERREMOVAL {
     output:
     tuple val(meta), path('*.fastq.gz'), emit: reads
     tuple val(meta), path('*.log')     , emit: log
-    path "*.version.txt"               , emit: version
+    path "versions.yml"                , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
 
     if (meta.single_end) {
@@ -41,7 +40,10 @@ process ADAPTERREMOVAL {
             --seed 42 \\
             --gzip \\
 
-        AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g" > ${software}.version.txt
+        cat <<-END_VERSIONS > versions.yml
+        ${getProcessName(task.process)}:
+            ${getSoftwareName(task.process)}: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
+        END_VERSIONS
         """
     } else if (!meta.single_end && !meta.collapse) {
         """
@@ -57,7 +59,10 @@ process ADAPTERREMOVAL {
             --seed 42 \\
             --gzip \\
 
-        AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g" > ${software}.version.txt
+        cat <<-END_VERSIONS > versions.yml
+        ${getProcessName(task.process)}:
+            ${getSoftwareName(task.process)}: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
+        END_VERSIONS
         """
     } else {
         """
@@ -73,7 +78,10 @@ process ADAPTERREMOVAL {
             --gzip \\
 
         cat *.collapsed.gz *.collapsed.truncated.gz > ${prefix}.merged.fastq.gz
-        AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g" > ${software}.version.txt
+        cat <<-END_VERSIONS > versions.yml
+        ${getProcessName(task.process)}:
+            ${getSoftwareName(task.process)}: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
+        END_VERSIONS
         """
     }
 

modules/adapterremoval/meta.yml

@@ -41,10 +41,10 @@ output:
         type: file
         description: AdapterRemoval log file
         pattern: "*.log"
-    - version:
+    - versions:
         type: file
-        description: File containing software version
+        description: File containing software versions
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 
 authors:
     - "@maxibor"

modules/agrvate/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/agrvate/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -24,16 +24,18 @@ process AGRVATE {
     output:
     tuple val(meta), path("${fasta.baseName}-results/${fasta.baseName}-summary.tab"), emit: summary
     path "${fasta.baseName}-results"                                                , emit: results_dir
-    path "*.version.txt"                                                            , emit: version
+    path "versions.yml"                                                             , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     agrvate \\
         $options.args \\
         -i $fasta
 
-    echo \$(agrvate -v 2>&1) | sed 's/agrvate //;' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo \$(agrvate -v 2>&1) | sed 's/agrvate v//;')
+    END_VERSIONS
     """
 }

modules/agrvate/meta.yml

@@ -38,9 +38,9 @@ output:
       type: directory
       description: Results of the agrvate assessement
       pattern: "*-results"
-  - version:
+  - versions:
       type: file
-      description: File containing software version
+      description: File containing software versions
-      pattern: "*.{version.txt}"
+      pattern: "versions.yml"
 authors:
   - "@abhi18av"

modules/allelecounter/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/allelecounter/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -24,10 +24,9 @@ process ALLELECOUNTER {
 
     output:
     tuple val(meta), path("*.alleleCount"), emit: allelecount
-    path "*.version.txt"                  , emit: version
+    path "versions.yml"                   , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     alleleCounter \\
@@ -36,6 +35,9 @@ process ALLELECOUNTER {
         -b $bam \\
         -o ${prefix}.alleleCount
 
-    alleleCounter --version > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(alleleCounter --version)
+    END_VERSIONS
     """
 }

modules/allelecounter/meta.yml

@@ -39,10 +39,10 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - version:
+  - versions:
       type: file
-      description: File containing software version
+      description: File containing software versions
-      pattern: "*.{version.txt}"
+      pattern: "versions.yml"
   - alleleCount:
       type: file
       description: Allele count file

modules/amps/functions.nf

@@ -0,0 +1,78 @@
+//
+//  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

@@ -0,0 +1,47 @@
+// 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 "https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1"
+    } else {
+        container "quay.io/biocontainers/hops:0.35--hdfd78af_1"
+    }
+
+    input:
+    path maltextract_results
+    path taxon_list
+    val filter
+
+    output:
+    path "results/heatmap_overview_Wevid.json" , emit: json
+    path "results/heatmap_overview_Wevid.pdf"  , emit: summary_pdf
+    path "results/heatmap_overview_Wevid.tsv"  , emit: tsv
+    path "results/pdf_candidate_profiles/"     , emit: candidate_pdfs
+    path "versions.yml"                        , emit: versions
+
+    script:
+    """
+    postprocessing.AMPS.r \\
+        -r $maltextract_results \\
+        -n $taxon_list \\
+        -m $filter \\
+        -t $task.cpus \\
+        -j \\
+        $options.args
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo \$(hops --version 2>&1) | sed 's/HOPS version//')
+    END_VERSIONS
+    """
+}

modules/amps/meta.yml

@@ -0,0 +1,66 @@
+name: amps
+description: Post-processing script of the MaltExtract component of the HOPS package
+keywords:
+  - malt
+  - MaltExtract
+  - HOPS
+  - amps
+  - alignment
+  - metagenomics
+  - ancient DNA
+  - aDNA
+  - palaeogenomics
+  - archaeogenomics
+  - microbiome
+  - authentication
+  - damage
+  - edit distance
+  - post Post-processing
+  - visualisation
+tools:
+  - amps:
+      description: Post-processing script of the MaltExtract tool for ancient metagenomics
+      homepage: "https://github.com/rhuebler/HOPS"
+      documentation: "https://github.com/keyfm/amps"
+      tool_dev_url: "https://github.com/keyfm/amps"
+      doi: "10.1186/s13059-019-1903-0"
+      licence: ['GPL >=3']
+
+input:
+  - maltextract_results:
+      type: directory
+      description: MaltExtract output directory
+      pattern: "results/"
+  - taxon_list:
+      type: file
+      description: List of target taxa to evaluate used in MaltExtract
+      pattern: "*.txt"
+  - filter:
+      type: string
+      description: The filter mode used in MaltExtract
+      pattern: "def_anc|default|scan|ancient|crawl"
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - json:
+      type: file
+      description: Candidate summary heatmap in MultiQC compatible JSON format
+      pattern: "heatmap_overview_Wevid.json"
+  - summary_pdf:
+      type: file
+      description: Candidate summary heatmap in PDF format
+      pattern: "heatmap_overview_Wevid.pdf"
+  - tsv:
+      type: file
+      description: Candidate summary heatmap in TSV format
+      pattern: "heatmap_overview_Wevid.tsv"
+  - candidate_pdfs:
+      type: directory
+      description: Directory of per sample output PDFs organised by reference
+      pattern: "pdf_candidate_profiles/"
+
+authors:
+  - "@jfy133"

modules/arriba/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/arriba/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -26,10 +26,9 @@ process ARRIBA {
     output:
     tuple val(meta), path("*.fusions.tsv")          , emit: fusions
     tuple val(meta), path("*.fusions.discarded.tsv"), emit: fusions_fail
-    path "*.version.txt"                            , emit: version
+    path "versions.yml"                             , emit: versions
 
     script:
-    def software  = getSoftwareName(task.process)
     def prefix    = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     def blacklist = (options.args.contains('-b')) ? '' : '-f blacklist'
     """
@@ -42,6 +41,9 @@ process ARRIBA {
         $blacklist \\
         $options.args
 
-    echo \$(arriba -h | grep 'Version:' 2>&1) |  sed 's/Version:\s//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(arriba -h | grep 'Version:' 2>&1 |  sed 's/Version:\s//')
+    END_VERSIONS
     """
 }

modules/arriba/meta.yml

@@ -37,10 +37,10 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - version:
+  - versions:
       type: file
-      description: File containing software version
+      description: File containing software versions
-      pattern: "*.{version.txt}"
+      pattern: "versions.yml"
   - fusions:
       type: file
       description: File contains fusions which pass all of Arriba's filters.

modules/artic/guppyplex/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/artic/guppyplex/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,10 +23,9 @@ process ARTIC_GUPPYPLEX {
 
     output:
     tuple val(meta), path("*.fastq.gz"), emit: fastq
-    path  "*.version.txt"              , emit: version
+    path  "versions.yml"               , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     artic \\
@@ -36,6 +35,9 @@ process ARTIC_GUPPYPLEX {
         --output ${prefix}.fastq
 
     pigz -p $task.cpus *.fastq
-    echo \$(artic --version 2>&1) | sed 's/^.*artic //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(artic --version 2>&1 | sed 's/^.*artic //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/artic/guppyplex/meta.yml

@@ -34,10 +34,10 @@ output:
       type: file
       description: Aggregated FastQ files
       pattern: "*.{fastq.gz}"
-  - version:
+  - versions:
       type: file
-      description: File containing software version
+      description: File containing software versions
-      pattern: "*.{version.txt}"
+      pattern: "versions.yml"
 
 authors:
   - "@joseespinosa"

modules/artic/minion/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/artic/minion/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -40,10 +40,9 @@ process ARTIC_MINION {
     tuple val(meta), path("${prefix}.pass.vcf.gz")                    , emit: vcf
     tuple val(meta), path("${prefix}.pass.vcf.gz.tbi")                , emit: tbi
     tuple val(meta), path("*.json"), optional:true                    , emit: json
-    path  "*.version.txt"                                             , emit: version
+    path  "versions.yml"                                              , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     prefix       = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     def version  = scheme_version.toString().toLowerCase().replaceAll('v','')
     def fast5    = params.fast5_dir          ? "--fast5-directory $fast5_dir"             : ""
@@ -68,6 +67,9 @@ process ARTIC_MINION {
         $scheme \\
         $prefix
 
-    echo \$(artic --version 2>&1) | sed 's/^.*artic //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(artic --version 2>&1 | sed 's/^.*artic //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/artic/minion/meta.yml

@@ -103,10 +103,10 @@ output:
       type: file
       description: JSON file for MultiQC
       pattern: "*.json"
-  - version:
+  - versions:
       type: file
-      description: File containing software version
+      description: File containing software versions
-      pattern: "*.{version.txt}"
+      pattern: "versions.yml"
 
 authors:
   - "@joseespinosa"

modules/bamaligncleaner/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/bamaligncleaner/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,10 +23,9 @@ process BAMALIGNCLEANER {
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
-    path "*.version.txt"          , emit: version
+    path "versions.yml"           , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
 
     """
@@ -35,6 +34,9 @@ process BAMALIGNCLEANER {
         -o ${prefix}.bam \\
         ${bam}
 
-    echo \$(bamAlignCleaner --version) | sed 's/.*version //' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bamAlignCleaner --version | sed 's/.*version //')
+    END_VERSIONS
     """
 }

modules/bamaligncleaner/meta.yml

@@ -27,10 +27,10 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - version:
+  - versions:
       type: file
-      description: File containing software version
+      description: File containing software versions
-      pattern: "*.{version.txt}"
+      pattern: "versions.yml"
   - bam:
       type: file
       description: Sorted BAM/CRAM file

modules/bamtools/split/functions.nf

@@ -0,0 +1,78 @@
+//
+//  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

@@ -0,0 +1,41 @@
+// 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 "https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9"
+    } else {
+        container "quay.io/biocontainers/bamtools:2.5.1--h9a82719_9"
+    }
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    path "versions.yml"           , emit: versions
+
+    script:
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    bamtools \\
+        split \\
+        -in $bam \\
+        $options.args
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        bamtools: \$( bamtools --version | grep -e 'bamtools' | sed 's/^.*bamtools //' )
+    END_VERSIONS
+    """
+}

modules/bamtools/split/meta.yml

@@ -0,0 +1,45 @@
+name: bamtools_split
+description: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
+keywords:
+  - bamtools
+  - bamtools/split
+  - bam
+  - split
+  - chunk
+tools:
+  - bamtools:
+      description: C++ API & command-line toolkit for working with BAM data
+      homepage: http://github.com/pezmaster31/bamtools
+      documentation: https://github.com/pezmaster31/bamtools/wiki
+      tool_dev_url: http://github.com/pezmaster31/bamtools
+      doi: ""
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: A BAM file to split
+      pattern: "*.bam"
+
+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: Several Bam files
+      pattern: "*.bam"
+
+authors:
+  - "@sguizard"

modules/bandage/image/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/bandage/image/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -24,15 +24,17 @@ process BANDAGE_IMAGE {
     output:
     tuple val(meta), path('*.png'), emit: png
     tuple val(meta), path('*.svg'), emit: svg
-    path  '*.version.txt'         , emit: version
+    path  "versions.yml"          , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     Bandage image $gfa ${prefix}.png $options.args
     Bandage image $gfa ${prefix}.svg $options.args
 
-    echo \$(Bandage --version 2>&1) | sed 's/^.*Version: //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo \$(Bandage --version 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/bandage/image/meta.yml

@@ -35,9 +35,9 @@ output:
         type: file
         description: Bandage image in SVG format
         pattern: "*.svg"
-    - version:
+    - versions:
         type: file
-        description: File containing software version
+        description: File containing software versions
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@heuermh"

modules/bbmap/align/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/bbmap/align/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -24,10 +24,9 @@ process BBMAP_ALIGN {
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
-    path "*.version.txt"          , emit: version
+    path "versions.yml"           , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
 
     input = meta.single_end ? "in=${fastq}" : "in=${fastq[0]} in2=${fastq[1]}"
@@ -54,6 +53,11 @@ process BBMAP_ALIGN {
         threads=$task.cpus \\
         -Xmx${task.memory.toGiga()}g
 
-    echo \$(bbversion.sh) > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(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/align/meta.yml

@@ -39,10 +39,10 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - version:
+  - versions:
       type: file
-      description: File containing software version
+      description: File containing software versions
-      pattern: "*.{version.txt}"
+      pattern: "versions.yml"
   - bam:
       type: file
       description: BAM file

modules/bbmap/bbduk/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/bbmap/bbduk/main.nf

@@ -1,4 +1,4 @@
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -24,10 +24,9 @@ process BBMAP_BBDUK {
     output:
     tuple val(meta), path('*.fastq.gz'), emit: reads
     tuple val(meta), path('*.log')     , emit: log
-    path '*.version.txt'               , emit: version
+    path "versions.yml"                , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     def raw      = meta.single_end ? "in=${reads[0]}" : "in1=${reads[0]} in2=${reads[1]}"
     def trimmed  = meta.single_end ? "out=${prefix}.fastq.gz" : "out1=${prefix}_1.fastq.gz out2=${prefix}_2.fastq.gz"
@@ -42,6 +41,9 @@ process BBMAP_BBDUK {
         $options.args \\
         $contaminants_fa \\
         &> ${prefix}.bbduk.log
-    echo \$(bbversion.sh) > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bbversion.sh)
+    END_VERSIONS
     """
 }

modules/bbmap/bbduk/meta.yml

@@ -39,10 +39,10 @@ output:
       type: file
       description: The trimmed/modified fastq reads
       pattern: "*fastq.gz"
-  - version:
+  - versions:
       type: file
-      description: File containing software version
+      description: File containing software versions
-      pattern: "*.{version.txt}"
+      pattern: "versions.yml"
   - log:
       type: file
       description: Bbduk log file

modules/bbmap/bbsplit/functions.nf

@@ -0,0 +1,78 @@
+//
+//  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

@@ -0,0 +1,94 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process BBMAP_BBSPLIT {
+    label 'process_high'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::bbmap=38.93" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bbmap:38.93--he522d1c_0"
+    } else {
+        container "quay.io/biocontainers/bbmap:38.93--he522d1c_0"
+    }
+
+    input:
+    tuple val(meta), path(reads)
+    path  index
+    path  primary_ref
+    tuple val(other_ref_names), path (other_ref_paths)
+    val   only_build_index
+
+    output:
+    path "bbsplit"                            , optional:true, emit: index
+    tuple val(meta), path('*primary*fastq.gz'), optional:true, emit: primary_fastq
+    tuple val(meta), path('*fastq.gz')        , optional:true, emit: all_fastq
+    tuple val(meta), path('*txt')             , optional:true, emit: stats
+    path "versions.yml"                       , emit: versions
+
+    script:
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[BBSplit] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+
+    def other_refs = []
+    other_ref_names.eachWithIndex { name, index ->
+        other_refs << "ref_${name}=${other_ref_paths[index]}"
+    }
+    if (only_build_index) {
+        if (primary_ref && other_ref_names && other_ref_paths) {
+            """
+            bbsplit.sh \\
+                -Xmx${avail_mem}g \\
+                ref_primary=$primary_ref \\
+                ${other_refs.join(' ')} \\
+                path=bbsplit \\
+                threads=$task.cpus \\
+                $options.args
+
+            cat <<-END_VERSIONS > versions.yml
+            ${getProcessName(task.process)}:
+                ${getSoftwareName(task.process)}: \$(bbversion.sh 2>&1)
+            END_VERSIONS
+            """
+        } else {
+            log.error 'ERROR: Please specify as input a primary fasta file along with names and paths to non-primary fasta files.'
+        }
+    } else {
+        def index_files = ''
+        if (index) {
+            index_files = "path=$index"
+        } else if (primary_ref && other_ref_names && other_ref_paths) {
+            index_files = "ref_primary=${primary_ref} ${other_refs.join(' ')}"
+        } else {
+            log.error 'ERROR: Please either specify a BBSplit index as input or a primary fasta file along with names and paths to non-primary fasta files.'
+        }
+        def fastq_in  = meta.single_end ? "in=${reads}" : "in=${reads[0]} in2=${reads[1]}"
+        def fastq_out = meta.single_end ? "basename=${prefix}_%.fastq.gz" : "basename=${prefix}_%_#.fastq.gz"
+        """
+        bbsplit.sh \\
+            -Xmx${avail_mem}g \\
+            $index_files \\
+            threads=$task.cpus \\
+            $fastq_in \\
+            $fastq_out \\
+            refstats=${prefix}.stats.txt \\
+            $options.args
+
+        cat <<-END_VERSIONS > versions.yml
+        ${getProcessName(task.process)}:
+            ${getSoftwareName(task.process)}: \$(bbversion.sh 2>&1)
+        END_VERSIONS
+        """
+    }
+}

modules/bbmap/bbsplit/meta.yml

@@ -0,0 +1,75 @@
+name: bbmap_bbsplit
+description: write your description here
+keywords:
+  - align
+  - map
+  - genome
+  - reference
+tools:
+  - bbmap:
+      description: BBMap is a short read aligner, as well as various other bioinformatic tools.
+      homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
+      documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
+      tool_dev_url: None
+      doi: ""
+      licence: ['UC-LBL license (see package)']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: |
+        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+        respectively.
+  - index:
+      type: directory
+      description: Directory to place generated index
+      pattern: "*"
+  - primary_ref:
+      type: path
+      description: Path to the primary reference
+      pattern: "*"
+  - other_ref_names:
+      type: list
+      description: List of other reference ids apart from the primary
+  - other_ref_paths:
+      type: list
+      description: Path to other references paths corresponding to "other_ref_names"
+  - only_build_index:
+      type: string
+      description: true = only build index; false = mapping
+
+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"
+  - index:
+      type: directory
+      description: Directory with index files
+      pattern: "bbsplit"
+  - primary_fastq:
+      type: file
+      description: Output reads that map to the primary reference
+      pattern: "*primary*fastq.gz"
+  - all_fastq:
+      type: file
+      description: All reads mapping to any of the references
+      pattern: "*fastq.gz"
+  - stats:
+      type: file
+      description: Tab-delimited text file containing mapping statistics
+      pattern: "*.txt"
+
+authors:
+  - "@joseespinosa"
+  - "@drpatelh"

modules/bbmap/index/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/bbmap/index/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,10 +23,9 @@ process BBMAP_INDEX {
 
     output:
     path 'ref'                    , emit: index
-    path "*.version.txt"          , emit: version
+    path "versions.yml"           , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     """
     bbmap.sh \\
         ref=${fasta} \\
@@ -34,6 +33,9 @@ process BBMAP_INDEX {
         threads=$task.cpus \\
         -Xmx${task.memory.toGiga()}g
 
-    echo \$(bbversion.sh) > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bbversion.sh)
+    END_VERSIONS
     """
 }

modules/bbmap/index/meta.yml

@@ -20,10 +20,10 @@ input:
       pattern: "*.{fna,fa,fasta}"
 
 output:
-  - version:
+  - versions:
       type: file
-      description: File containing software version
+      description: File containing software versions
-      pattern: "*.{version.txt}"
+      pattern: "versions.yml"
   - db:
       type: directory
       description: Directory with index files

modules/bcftools/concat/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/bcftools/concat/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,10 +23,9 @@ process BCFTOOLS_CONCAT {
 
     output:
     tuple val(meta), path("*.gz"), emit: vcf
-    path  "*.version.txt"        , emit: version
+    path  "versions.yml"         , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     prefix       = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     bcftools concat \\
@@ -35,6 +34,9 @@ process BCFTOOLS_CONCAT {
         --threads $task.cpus \\
         ${vcfs}
 
-    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/bcftools/concat/meta.yml

@@ -34,9 +34,9 @@ output:
         type: file
         description: VCF concatenated output file
         pattern: "*.{vcf.gz}"
-    - version:
+    - versions:
         type: file
-        description: File containing software version
+        description: File containing software versions
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
   - "@abhi18av"

modules/bcftools/consensus/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/bcftools/consensus/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,16 +23,18 @@ process BCFTOOLS_CONSENSUS {
 
     output:
     tuple val(meta), path('*.fa'), emit: fasta
-    path  '*.version.txt'        , emit: version
+    path  "versions.yml"         , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     cat $fasta | bcftools consensus $vcf $options.args > ${prefix}.fa
     header=\$(head -n 1 ${prefix}.fa | sed 's/>//g')
     sed -i 's/\${header}/${meta.id}/g' ${prefix}.fa
 
-    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/bcftools/consensus/meta.yml

@@ -39,10 +39,10 @@ output:
         type: file
         description: FASTA reference consensus file
         pattern: "*.{fasta,fa}"
-    - version:
+    - versions:
         type: file
-        description: File containing software version
+        description: File containing software versions
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@joseespinosa"
     - "@drpatelh"

modules/bcftools/filter/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/bcftools/filter/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,10 +23,9 @@ process BCFTOOLS_FILTER {
 
     output:
     tuple val(meta), path("*.gz"), emit: vcf
-    path  "*.version.txt"        , emit: version
+    path  "versions.yml"         , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     bcftools filter \\
@@ -34,6 +33,9 @@ process BCFTOOLS_FILTER {
         $options.args \\
         $vcf
 
-    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/bcftools/filter/meta.yml

@@ -31,10 +31,10 @@ output:
         type: file
         description: VCF filtered output file
         pattern: "*.{vcf}"
-    - version:
+    - versions:
         type: file
-        description: File containing software version
+        description: File containing software versions
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@joseespinosa"
     - "@drpatelh"

modules/bcftools/index/functions.nf

@@ -0,0 +1,78 @@
+//
+//  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

@@ -0,0 +1,44 @@
+// 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 "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
+    } else {
+        container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
+    }
+
+    input:
+    tuple val(meta), path(vcf)
+
+    output:
+    tuple val(meta), path("*.csi"), optional:true, emit: csi
+    tuple val(meta), path("*.tbi"), optional:true, emit: tbi
+    path "versions.yml"          , emit: version
+
+    script:
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+
+    """
+    bcftools \\
+        index \\
+        $options.args \\
+        --threads $task.cpus \\
+        $vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
+    """
+}

modules/bcftools/index/meta.yml

@@ -0,0 +1,49 @@
+name: bcftools_index
+description: Index VCF tools
+keywords:
+  - vcf
+  - index
+  - bcftools
+  - csi
+  - tbi
+tools:
+  - bcftools:
+      description: BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.  Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
+      homepage: https://samtools.github.io/bcftools/
+      documentation: https://samtools.github.io/bcftools/howtos/index.html
+      tool_dev_url: https://github.com/samtools/bcftools
+      doi: "10.1093/gigascience/giab008"
+      licence: ['GPL']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - VCF:
+      type: file
+      description: VCF file (optionally GZIPPED)
+      pattern: "*.{vcf,vcf.gz}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "versions.yml"
+  - csi:
+      type: file
+      description: Default VCF file index file
+      pattern: "*.csi"
+  - tbi:
+      type: file
+      description: Alternative VCF file index file for larger files (activated with -t parameter)
+      pattern: "*.tbi"
+
+authors:
+  - "@jfy133"

modules/bcftools/isec/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/bcftools/isec/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,16 +23,18 @@ process BCFTOOLS_ISEC {
 
     output:
     tuple val(meta), path("${prefix}"), emit: results
-    path  "*.version.txt"             , emit: version
+    path  "versions.yml"              , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     prefix       = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     bcftools isec  \\
         $options.args \\
         -p $prefix \\
         *.vcf.gz
-    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/bcftools/isec/meta.yml

@@ -39,10 +39,10 @@ output:
         type: directory
         description: Folder containing the set operations results perform on the vcf files
         pattern: "${prefix}"
-    - version:
+    - versions:
         type: file
-        description: File containing software version
+        description: File containing software versions
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@joseespinosa"
     - "@drpatelh"

modules/bcftools/merge/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/bcftools/merge/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,16 +23,18 @@ process BCFTOOLS_MERGE {
 
     output:
     tuple val(meta), path("*.gz"), emit: vcf
-    path  "*.version.txt"        , emit: version
+    path  "versions.yml"         , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     prefix       = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     bcftools merge -Oz \\
         --output ${prefix}.vcf.gz \\
         $options.args \\
         *.vcf.gz
-    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/bcftools/merge/meta.yml

@@ -37,10 +37,10 @@ output:
         type: file
         description: VCF merged output file
         pattern: "*.{vcf.gz}"
-    - version:
+    - versions:
         type: file
-        description: File containing software version
+        description: File containing software versions
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@joseespinosa"
     - "@drpatelh"

modules/bcftools/mpileup/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/bcftools/mpileup/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -26,10 +26,9 @@ process BCFTOOLS_MPILEUP {
     tuple val(meta), path("*.gz")      , emit: vcf
     tuple val(meta), path("*.tbi")     , emit: tbi
     tuple val(meta), path("*stats.txt"), emit: stats
-    path  "*.version.txt"              , emit: version
+    path  "versions.yml"               , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     echo "${meta.id}" > sample_name.list
@@ -42,6 +41,9 @@ process BCFTOOLS_MPILEUP {
         | bcftools view --output-file ${prefix}.vcf.gz --output-type z $options.args3
     tabix -p vcf -f ${prefix}.vcf.gz
     bcftools stats ${prefix}.vcf.gz > ${prefix}.bcftools_stats.txt
-    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/bcftools/mpileup/meta.yml

@@ -43,10 +43,10 @@ output:
         type: file
         description: Text output file containing stats
         pattern: "*{stats.txt}"
-    - version:
+    - versions:
         type: file
-        description: File containing software version
+        description: File containing software versions
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@joseespinosa"
     - "@drpatelh"

modules/bcftools/norm/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/bcftools/norm/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -24,10 +24,9 @@ process BCFTOOLS_NORM {
 
     output:
     tuple val(meta), path("*.gz") , emit: vcf
-    path "*.version.txt"          , emit: version
+    path "versions.yml"           , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     bcftools norm \\
@@ -37,6 +36,9 @@ process BCFTOOLS_NORM {
         --threads $task.cpus \\
         ${vcf}
 
-    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/bcftools/norm/meta.yml

@@ -37,9 +37,9 @@ output:
         type: file
         description: VCF normalized output file
         pattern: "*.{vcf.gz}"
-    - version:
+    - versions:
         type: file
-        description: File containing software version
+        description: File containing software versions
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@abhi18av"

modules/bcftools/query/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/bcftools/query/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -26,10 +26,9 @@ process BCFTOOLS_QUERY {
 
     output:
     tuple val(meta), path("*.gz") , emit: vcf
-    path "*.version.txt"          , emit: version
+    path "versions.yml"           , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     def regions_file  = regions ? "--regions-file ${regions}" : ""
     def targets_file = targets ? "--targets-file ${targets}" : ""
@@ -44,6 +43,9 @@ process BCFTOOLS_QUERY {
         $options.args \\
         ${vcf}
 
-    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/bcftools/query/meta.yml

@@ -53,9 +53,9 @@ output:
         type: file
         description: VCF query output file
         pattern: "*.{vcf.gz}"
-    - version:
+    - versions:
         type: file
-        description: File containing software version
+        description: File containing software versions
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
   - "@abhi18av"

modules/bcftools/reheader/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/bcftools/reheader/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -25,10 +25,9 @@ process BCFTOOLS_REHEADER {
 
     output:
     tuple val(meta), path("*.vcf.gz"), emit: vcf
-    path "*.version.txt"             , emit: version
+    path "versions.yml"              , emit: versions
 
     script:
-    def software         = getSoftwareName(task.process)
     def prefix           = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     def update_sequences = fai ? "-f $fai" : ""
     def new_header       = header ? "-h $header" : ""
@@ -42,6 +41,9 @@ process BCFTOOLS_REHEADER {
         -o ${prefix}.vcf.gz \\
         $vcf
 
-    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/bcftools/reheader/meta.yml

@@ -38,10 +38,10 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - version:
+  - versions:
       type: file
-      description: File containing software version
+      description: File containing software versions
-      pattern: "*.{version.txt}"
+      pattern: "versions.yml"
   - vcf:
       type: file
       description: VCF with updated header

modules/bcftools/stats/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/bcftools/stats/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,13 +23,15 @@ process BCFTOOLS_STATS {
 
     output:
     tuple val(meta), path("*stats.txt"), emit: stats
-    path  "*.version.txt"              , emit: version
+    path  "versions.yml"               , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     bcftools stats $options.args $vcf > ${prefix}.bcftools_stats.txt
-    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/bcftools/stats/meta.yml

@@ -32,10 +32,10 @@ output:
         type: file
         description: Text output file containing stats
         pattern: "*_{stats.txt}"
-    - version:
+    - versions:
         type: file
-        description: File containing software version
+        description: File containing software versions
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@joseespinosa"
     - "@drpatelh"

modules/bcftools/view/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/bcftools/view/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -26,10 +26,9 @@ process BCFTOOLS_VIEW {
 
     output:
     tuple val(meta), path("*.gz") , emit: vcf
-    path "*.version.txt"          , emit: version
+    path "versions.yml"           , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     def regions_file  = regions ? "--regions-file ${regions}" : ""
     def targets_file = targets ? "--targets-file ${targets}" : ""
@@ -46,6 +45,9 @@ process BCFTOOLS_VIEW {
         --threads $task.cpus \\
         ${vcf}
 
-    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/bcftools/view/meta.yml

@@ -54,9 +54,9 @@ output:
         type: file
         description: VCF normalized output file
         pattern: "*.{vcf.gz}"
-    - version:
+    - versions:
         type: file
-        description: File containing software version
+        description: File containing software versions
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@abhi18av"

modules/bedtools/bamtobed/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/bedtools/bamtobed/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,10 +23,9 @@ process BEDTOOLS_BAMTOBED {
 
     output:
     tuple val(meta), path("*.bed"), emit: bed
-    path  "*.version.txt"         , emit: version
+    path  "versions.yml"          , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     bedtools \\
@@ -35,6 +34,9 @@ process BEDTOOLS_BAMTOBED {
         -i $bam \\
         | bedtools sort > ${prefix}.bed
 
-    bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+    END_VERSIONS
     """
 }

modules/bedtools/bamtobed/meta.yml

@@ -28,10 +28,10 @@ output:
         type: file
         description: Bed file containing genomic intervals.
         pattern: "*.{bed}"
-    - version:
+    - versions:
         type: file
-        description: File containing software version
+        description: File containing software versions
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@yuukiiwa"
     - "@drpatelh"

modules/bedtools/complement/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/bedtools/complement/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -24,10 +24,9 @@ process BEDTOOLS_COMPLEMENT {
 
     output:
     tuple val(meta), path('*.bed'), emit: bed
-    path  '*.version.txt'         , emit: version
+    path  "versions.yml"          , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     bedtools \\
@@ -37,6 +36,9 @@ process BEDTOOLS_COMPLEMENT {
         $options.args \\
         > ${prefix}.bed
 
-    bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+    END_VERSIONS
     """
 }

modules/bedtools/complement/meta.yml

@@ -32,10 +32,10 @@ output:
         type: file
         description: Bed file with all genomic intervals that are not covered by at least one record from the input file.
         pattern: "*.{bed}"
-    - version:
+    - versions:
         type: file
-        description: File containing software version
+        description: File containing software versions
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@Emiller88"
     - "@sruthipsuresh"

modules/bedtools/genomecov/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/bedtools/genomecov/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -25,10 +25,9 @@ process BEDTOOLS_GENOMECOV {
 
     output:
     tuple val(meta), path("*.${extension}"), emit: genomecov
-    path  "*.version.txt"                  , emit: version
+    path  "versions.yml"                   , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     if (intervals.name =~ /\.bam/) {
         """
@@ -38,7 +37,10 @@ process BEDTOOLS_GENOMECOV {
             $options.args \\
             > ${prefix}.${extension}
 
-        bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
+        cat <<-END_VERSIONS > versions.yml
+        ${getProcessName(task.process)}:
+            ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+        END_VERSIONS
         """
     } else {
         """
@@ -49,7 +51,10 @@ process BEDTOOLS_GENOMECOV {
             $options.args \\
             > ${prefix}.${extension}
 
-        bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
+        cat <<-END_VERSIONS > versions.yml
+        ${getProcessName(task.process)}:
+            ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+        END_VERSIONS
         """
     }
 }

modules/bedtools/genomecov/meta.yml

@@ -35,10 +35,10 @@ output:
         type: file
         description: Computed genome coverage file
         pattern: "*.${extension}"
-    - version:
+    - versions:
         type: file
-        description: File containing software version
+        description: File containing software versions
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@Emiller88"
     - "@sruthipsuresh"

modules/bedtools/getfasta/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/bedtools/getfasta/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -24,10 +24,9 @@ process BEDTOOLS_GETFASTA {
 
     output:
     path "*.fa"         , emit: fasta
-    path "*.version.txt", emit: version
+    path "versions.yml" , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${bed.baseName}${options.suffix}" : "${bed.baseName}"
     """
     bedtools \\
@@ -37,6 +36,9 @@ process BEDTOOLS_GETFASTA {
         -bed $bed \\
         -fo ${prefix}.fa
 
-    bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+    END_VERSIONS
     """
 }

modules/bedtools/getfasta/meta.yml

@@ -24,10 +24,10 @@ output:
         type: file
         description: Output fasta file with extracted sequences
         pattern: "*.{fa}"
-    - version:
+    - versions:
         type: file
-        description: File containing software version
+        description: File containing software versions
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@joseespinosa"
     - "@drpatelh"

modules/bedtools/intersect/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
+    def ioptions  = initOptions(args.options)
-        def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
-        if (ioptions.publish_by_meta) {
+    // Do not publish versions.yml unless running from pytest workflow
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-            for (key in key_list) {
+        return null
-                if (args.meta && key instanceof String) {
+    }
-                    def path = key
+    if (ioptions.publish_by_meta) {
-                    if (args.meta.containsKey(key)) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+        for (key in key_list) {
-                    }
+            if (args.meta && key instanceof String) {
-                    path = path instanceof String ? path : ''
+                def path = key
-                    path_list.add(path)
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
+    }
-            for (ext in ioptions.publish_files) {
+    if (ioptions.publish_files instanceof Map) {
-                if (args.filename.endsWith(ext.key)) {
+        for (ext in ioptions.publish_files) {
-                    def ext_list = path_list.collect()
+            if (args.filename.endsWith(ext.key)) {
-                    ext_list.add(ext.value)
+                def ext_list = path_list.collect()
-                    return "${getPathFromList(ext_list)}/$args.filename"
+                ext_list.add(ext.value)
-                }
+                return "${getPathFromList(ext_list)}/$args.filename"
-            }
+            }
-        } else if (ioptions.publish_files == null) {
+        }
-            return "${getPathFromList(path_list)}/$args.filename"
+    } else if (ioptions.publish_files == null) {
-        }
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }

modules/bedtools/intersect/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -24,10 +24,9 @@ process BEDTOOLS_INTERSECT {
 
     output:
     tuple val(meta), path("*.${extension}"), emit: intersect
-    path  '*.version.txt'                  , emit: version
+    path  "versions.yml"                   , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     bedtools \\
@@ -37,6 +36,9 @@ process BEDTOOLS_INTERSECT {
         $options.args \\
         > ${prefix}.${extension}
 
-    bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+    END_VERSIONS
     """
 }