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

.github/workflows/bowtie_align.yml

@@ -0,0 +1,42 @@
+name: bowtie_align
+on:
+    push:
+        paths:
+            - software/bowtie/align/**
+            - software/bowtie/index/**
+            - .github/workflows/bowtie_align.yml
+            - tests/software/bowtie/**
+    pull_request:
+        paths:
+            - software/bowtie/align/**
+            - software/bowtie/index/**
+            - .github/workflows/bowtie_align.yml
+            - tests/software/bowtie/**
+
+jobs:
+    ci_test:
+        runs-on: ubuntu-latest
+        strategy:
+            matrix:
+                nxf_version: [20.11.0-edge]
+        env:
+            NXF_ANSI_LOG: false
+        steps:
+            - uses: actions/checkout@v2
+
+            - name: Install Nextflow
+              env:
+                  NXF_VER: ${{ matrix.nxf_version }}
+              run: |
+                  wget -qO- get.nextflow.io | bash
+                  sudo mv nextflow /usr/local/bin/
+
+            - name: Set up Python
+              uses: actions/setup-python@v2
+              with:
+                  python-version: "3.x"
+            - name: Install dependencies
+              run: python -m pip install --upgrade pip pytest-workflow
+
+            # Test the module
+            - run: pytest --tag bowtie_align --symlink --wt 2

.github/workflows/bowtie_index.yml

@@ -0,0 +1,40 @@
+name: bowtie_index
+on:
+  push:
+    paths:
+      - software/bowtie/index/**
+      - .github/workflows/bowtie_index.yml
+      - tests/software/bowtie/**
+  pull_request:
+    paths:
+      - software/bowtie/index/**
+      - .github/workflows/bowtie_index.yml
+      - tests/software/bowtie/**
+
+jobs:
+  ci_test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        nxf_version: [20.11.0-edge]
+    env:
+      NXF_ANSI_LOG: false
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          NXF_VER: ${{ matrix.nxf_version }}
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
+
+      # Test the module
+      - run: pytest --tag bowtie_index --symlink --wt 2

.github/workflows/linting.yml

@@ -17,20 +17,20 @@ jobs:
       - name: Run Markdownlint
         run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.markdownlint.yml
 
-  # EditorConfig:
+  EditorConfig:
-  #   runs-on: ubuntu-latest
+    runs-on: ubuntu-latest
-  #   steps:
+    steps:
-  #     - uses: actions/checkout@v2
+      - uses: actions/checkout@v2
 
-  #     - uses: actions/setup-node@v1
+      - uses: actions/setup-node@v1
-  #       with:
+        with:
-  #         node-version: "10"
+          node-version: "10"
 
-  #     - name: Install ECLint
+      - name: Install editorconfig-checker
-  #       run: npm install -g eclint
+        run: npm install -g editorconfig-checker
 
-  #     - name: Run ECLint check
+      - name: Run ECLint check
-  #       run: eclint check $(git ls-files | grep -v test)
+        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
 
   YAML:
     runs-on: ubuntu-latest

deprecated/bedtools/intersect/main.nf

@@ -34,4 +34,3 @@ process INTERSECT_BED {
     bedtools --version | sed -n "s/.*\\(v.*\$\\)/\\1/p" > bedtools.version.txt
     """
 }
-

software/SOFTWARE/TOOL/functions.nf

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

software/SOFTWARE/TOOL/main.nf

@@ -50,7 +50,7 @@ process SOFTWARE_TOOL {
     } else {
         container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
     }
-    
+
     input:
     // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
     //               MUST be provided as an input via a Groovy Map called "meta".
@@ -59,7 +59,7 @@ process SOFTWARE_TOOL {
     // TODO nf-core: Where applicable please provide/convert compressed files as input/output
     //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
     tuple val(meta), path(reads)
-    
+
     output:
     // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
     // TODO nf-core: If meta is provided in "input:" section then it MUST be added to ALL output channels (except version)

software/bowtie/align/functions.nf

@@ -0,0 +1,60 @@
+
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", '') } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/bowtie/align/main.nf

@@ -0,0 +1,59 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process BOWTIE_ALIGN {
+    tag "$meta.id"
+    label 'process_high'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.10' : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container 'https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0'
+    } else {
+        container 'quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0'
+    }
+
+    input:
+    tuple val(meta), path(reads)
+    path  index
+
+    output:
+    tuple val(meta), path('*.bam'), emit: bam
+    tuple val(meta), path('*.out'), emit: log
+    path  '*.version.txt'         , emit: version
+    tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq
+
+    script:
+    def software  = getSoftwareName(task.process)
+    def prefix    = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def unaligned = params.save_unaligned ? "--un ${prefix}.unmapped.fastq" : ''
+    def endedness = meta.single_end ? "$reads" : "-1 ${reads[0]} -2 ${reads[1]}"
+    """
+    INDEX=`find -L ./ -name "*.3.ebwt" | sed 's/.3.ebwt//'`
+    bowtie \\
+        --threads $task.cpus \\
+        --sam \\
+        -x \$INDEX \\
+        -q \\
+        $unaligned \\
+        $options.args \\
+        $endedness \\
+        2> ${prefix}.out \\
+        | samtools view $options.args2 -@ $task.cpus -bS -o ${prefix}.bam -
+
+    if [ -f ${prefix}.unmapped.fastq ]; then
+        gzip ${prefix}.unmapped.fastq
+    fi
+    if [ -f ${prefix}.unmapped_1.fastq ]; then
+        gzip ${prefix}.unmapped_1.fastq
+        gzip ${prefix}.unmapped_2.fastq
+    fi
+
+    echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//' > ${software}.version.txt
+    """
+}

software/bowtie/align/meta.yml

@@ -0,0 +1,69 @@
+name: bowtie_align
+description: Align reads to a reference genome using bowtie
+keywords:
+    - align
+    - fasta
+    - genome
+    - reference
+tools:
+    - bowtie:
+          description: |
+              bowtie is a software package for mapping DNA sequences against
+              a large reference genome, such as the human genome.
+          homepage: http://bowtie-bio.sourceforge.net/index.shtml
+          documentation: http://bowtie-bio.sourceforge.net/manual.shtml
+          arxiv: arXiv:1303.3997
+params:
+    - outdir:
+          type: string
+          description: |
+              The pipeline's output directory. By default, the module will
+              output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+          type: string
+          description: |
+              Value for the Nextflow `publishDir` mode parameter.
+              Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - enable_conda:
+          type: boolean
+          description: |
+              Run the module with Conda using the software specified
+              via the `conda` directive
+    - singularity_pull_docker_container:
+          type: boolean
+          description: |
+              Instead of directly downloading Singularity images for use with Singularity,
+              force the workflow to pull and convert Docker containers instead.
+    - save_unaligned:
+          type: boolean
+          description: Save unaligned reads
+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: file
+          description: Bowtie genome index files
+          pattern: "*.ebwt"
+output:
+    - bam:
+          type: file
+          description: Output BAM file containing read alignments
+          pattern: "*.{bam}"
+    - version:
+          type: file
+          description: File containing software version
+          pattern: "*.{version.txt}"
+    - fastq:
+          type: file
+          description: Unaligned FastQ files
+          pattern: "*.fastq.gz"
+authors:
+    - "@kevinmenden"

software/bowtie/index/functions.nf

@@ -0,0 +1,60 @@
+
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", '') } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/bowtie/index/main.nf

@@ -0,0 +1,35 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process BOWTIE_INDEX {
+    tag "$fasta"
+    label 'process_high'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+
+    conda (params.enable_conda ? 'bioconda::bowtie=1.3.0' : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container 'https://depot.galaxyproject.org/singularity/bowtie:1.3.0--py38hed8969a_1'
+    } else {
+        container 'quay.io/biocontainers/bowtie:1.3.0--py38hed8969a_1'
+    }
+
+    input:
+    path fasta
+
+    output:
+    path 'bowtie', emit: index
+    path '*.version.txt', emit: version
+
+    script:
+    def software  = getSoftwareName(task.process)
+    """
+    mkdir bowtie
+    bowtie-build --threads $task.cpus $fasta bowtie/${fasta.baseName}
+    echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//' > ${software}.version.txt
+    """
+}

software/bowtie/index/meta.yml

@@ -0,0 +1,51 @@
+name: bowtie_index
+description: Create bowtie index for reference genome
+keywords:
+    - index
+    - fasta
+    - genome
+    - reference
+tools:
+    - bowtie:
+          description: |
+              bowtie is a software package for mapping DNA sequences against
+              a large reference genome, such as the human genome.
+          homepage: http://bowtie-bio.sourceforge.net/index.shtml
+          documentation: http://bowtie-bio.sourceforge.net/manual.shtml
+          arxiv: arXiv:1303.3997
+params:
+    - outdir:
+          type: string
+          description: |
+              The pipeline's output directory. By default, the module will
+              output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+          type: string
+          description: |
+              Value for the Nextflow `publishDir` mode parameter.
+              Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - enable_conda:
+          type: boolean
+          description: |
+              Run the module with Conda using the software specified
+              via the `conda` directive
+    - singularity_pull_docker_container:
+          type: boolean
+          description: |
+              Instead of directly downloading Singularity images for use with Singularity,
+              force the workflow to pull and convert Docker containers instead.
+input:
+    - fasta:
+          type: file
+          description: Input genome fasta file
+output:
+    - index:
+          type: file
+          description: Bowtie genome index files
+          pattern: "*.ebwt"
+    - version:
+          type: file
+          description: File containing software version
+          pattern: "*.{version.txt}"
+authors:
+    - "@kevinmenden"

software/bwa/index/functions.nf

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

software/bwa/index/main.nf

@@ -20,7 +20,7 @@ process BWA_INDEX {
 
     input:
     path fasta
-    
+
     output:
     path "${fasta}.*"   , emit: index
     path "*.version.txt", emit: version

software/bwa/mem/functions.nf

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

software/bwa/mem/main.nf

@@ -17,12 +17,12 @@ process BWA_MEM {
     } else {
         container "quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0"
     }
-    
+
     input:
     tuple val(meta), path(reads)
     path  index
     path  fasta
-    
+
     output:
     tuple val(meta), path("*.bam"), emit: bam
     path  "*.version.txt"         , emit: version

software/deeptools/computematrix/functions.nf

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

software/deeptools/computematrix/main.nf

@@ -21,7 +21,7 @@ process DEEPTOOLS_COMPUTEMATRIX {
     input:
     tuple val(meta), path(bigwig)
     path  bed
-    
+
     output:
     tuple val(meta), path("*.mat.gz") , emit: matrix
     tuple val(meta), path("*.mat.tab"), emit: table

software/deeptools/plotfingerprint/functions.nf

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

software/deeptools/plotfingerprint/main.nf

@@ -20,7 +20,7 @@ process DEEPTOOLS_PLOTFINGERPRINT {
 
     input:
     tuple val(meta), path(bams), path(bais)
-    
+
     output:
     tuple val(meta), path("*.pdf")          , emit: pdf
     tuple val(meta), path("*.raw.txt")      , emit: matrix

software/deeptools/plotheatmap/functions.nf

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

software/deeptools/plotheatmap/main.nf

@@ -20,7 +20,7 @@ process DEEPTOOLS_PLOTHEATMAP {
 
     input:
     tuple val(meta), path(matrix)
-    
+
     output:
     tuple val(meta), path("*.pdf"), emit: pdf
     tuple val(meta), path("*.tab"), emit: table

software/deeptools/plotprofile/functions.nf

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

software/deeptools/plotprofile/main.nf

@@ -20,7 +20,7 @@ process DEEPTOOLS_PLOTPROFILE {
 
     input:
     tuple val(meta), path(matrix)
-    
+
     output:
     tuple val(meta), path("*.pdf"), emit: pdf
     tuple val(meta), path("*.tab"), emit: table

software/fastqc/functions.nf

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

software/fastqc/main.nf

@@ -17,10 +17,10 @@ process FASTQC {
     } else {
         container "quay.io/biocontainers/fastqc:0.11.9--0"
     }
-    
+
     input:
     tuple val(meta), path(reads)
-    
+
     output:
     tuple val(meta), path("*.html"), emit: html
     tuple val(meta), path("*.zip") , emit: zip

software/gffread/functions.nf

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

software/gffread/main.nf

@@ -1,33 +1,33 @@
-// Import generic module functions
+// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
-
+
-params.options = [:]
+params.options = [:]
-def options    = initOptions(params.options)
+def options    = initOptions(params.options)
-
+
-process GFFREAD {
+process GFFREAD {
-    tag "$gff"
+    tag "$gff"
-    publishDir "${params.outdir}",
+    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
+        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
-
+
-    conda (params.enable_conda ? "bioconda::gffread=0.12.1" : null)
+    conda (params.enable_conda ? "bioconda::gffread=0.12.1" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0"
+        container "https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0"
-    } else {
+    } else {
-        container "quay.io/biocontainers/gffread:0.12.1--h8b12597_0"
+        container "quay.io/biocontainers/gffread:0.12.1--h8b12597_0"
-    }
+    }
-
+
-    input:
+    input:
-    path gff
+    path gff
-    
+
-    output:
+    output:
-    path "*.gtf"        , emit: gtf
+    path "*.gtf"        , emit: gtf
-    path "*.version.txt", emit: version
+    path "*.version.txt", emit: version
-
+
-    script:
+    script:
-    def software = getSoftwareName(task.process)
+    def software = getSoftwareName(task.process)
-    """
+    """
-    gffread $gff $options.args -o ${gff.baseName}.gtf
+    gffread $gff $options.args -o ${gff.baseName}.gtf
-    echo \$(gffread --version 2>&1) > ${software}.version.txt
+    echo \$(gffread --version 2>&1) > ${software}.version.txt
-    """
+    """
-}
+}

software/hisat2/align/functions.nf

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

software/hisat2/align/main.nf

@@ -19,12 +19,12 @@ process HISAT2_ALIGN {
     } else {
         container "quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0"
     }
-    
+
     input:
     tuple val(meta), path(reads)
     path  index
     path  splicesites
-    
+
     output:
     tuple val(meta), path("*.bam"), emit: bam
     tuple val(meta), path("*.log"), emit: summary

software/hisat2/build/functions.nf

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

software/hisat2/build/main.nf

@@ -1,67 +1,67 @@
-// Import generic module functions
+// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
-
+
-params.options = [:]
+params.options = [:]
-def options    = initOptions(params.options)
+def options    = initOptions(params.options)
-
+
-def VERSION = '2.2.0'
+def VERSION = '2.2.0'
-
+
-process HISAT2_BUILD {
+process HISAT2_BUILD {
-    tag "$fasta"
+    tag "$fasta"
-    publishDir "${params.outdir}",
+    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
+        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
-
+
-    conda (params.enable_conda ? "bioconda::hisat2=2.2.0" : null)
+    conda (params.enable_conda ? "bioconda::hisat2=2.2.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
+        container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
-    } else {
+    } else {
-        container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
+        container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
-    }
+    }
-
+
-    input:
+    input:
-    path fasta
+    path fasta
-    path gtf
+    path gtf
-    path splicesites
+    path splicesites
-
+
-    output:
+    output:
-    path "hisat2",        emit: index
+    path "hisat2",        emit: index
-    path "*.version.txt", emit: version
+    path "*.version.txt", emit: version
-
+
-    script:
+    script:
-    def avail_mem = 0
+    def avail_mem = 0
-    if (!task.memory) {
+    if (!task.memory) {
-        log.info "[HISAT2 index build] Available memory not known - defaulting to 0. Specify process memory requirements to change this."
+        log.info "[HISAT2 index build] Available memory not known - defaulting to 0. Specify process memory requirements to change this."
-    } else {
+    } else {
-        log.info "[HISAT2 index build] Available memory: ${task.memory}"
+        log.info "[HISAT2 index build] Available memory: ${task.memory}"
-        avail_mem = task.memory.toGiga()
+        avail_mem = task.memory.toGiga()
-    }
+    }
-
+
-    def extract_exons = ''
+    def extract_exons = ''
-    def ss = ''
+    def ss = ''
-    def exon = ''
+    def exon = ''
-    if (avail_mem > params.hisat_build_memory) {
+    if (avail_mem > params.hisat_build_memory) {
-        log.info "[HISAT2 index build] Over ${params.hisat_build_memory} GB available, so using splice sites and exons in HISAT2 index"
+        log.info "[HISAT2 index build] Over ${params.hisat_build_memory} GB available, so using splice sites and exons in HISAT2 index"
-        extract_exons = "hisat2_extract_exons.py $gtf > ${gtf.baseName}.exons.txt"
+        extract_exons = "hisat2_extract_exons.py $gtf > ${gtf.baseName}.exons.txt"
-        ss = "--ss $splicesites"
+        ss = "--ss $splicesites"
-        exon = "--exon ${gtf.baseName}.exons.txt"
+        exon = "--exon ${gtf.baseName}.exons.txt"
-    } else {
+    } else {
-        log.info "[HISAT2 index build] Less than ${params.hisat_build_memory} GB available, so NOT using splice sites and exons in HISAT2 index."
+        log.info "[HISAT2 index build] Less than ${params.hisat_build_memory} GB available, so NOT using splice sites and exons in HISAT2 index."
-        log.info "[HISAT2 index build] Use --hisat_build_memory [small number] to skip this check."
+        log.info "[HISAT2 index build] Use --hisat_build_memory [small number] to skip this check."
-    }
+    }
-
+
-    def software = getSoftwareName(task.process)
+    def software = getSoftwareName(task.process)
-    """
+    """
-    mkdir hisat2
+    mkdir hisat2
-    $extract_exons
+    $extract_exons
-    hisat2-build \\
+    hisat2-build \\
-        -p $task.cpus \\
+        -p $task.cpus \\
-        $ss \\
+        $ss \\
-        $exon \\
+        $exon \\
-        $options.args \\
+        $options.args \\
-        $fasta \\
+        $fasta \\
-        hisat2/${fasta.baseName}
+        hisat2/${fasta.baseName}
-
+
-    echo $VERSION > ${software}.version.txt
+    echo $VERSION > ${software}.version.txt
-    """
+    """
-}
+}

software/hisat2/extractsplicesites/functions.nf

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

software/hisat2/extractsplicesites/main.nf

@@ -17,7 +17,7 @@ process HISAT2_EXTRACTSPLICESITES {
     } else {
         container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
     }
-    
+
     input:
     path gtf
 

software/homer/annotatepeaks/functions.nf

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

software/lib/functions.nf

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

software/macs2/callpeak/functions.nf

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

software/macs2/callpeak/main.nf

@@ -21,7 +21,7 @@ process MACS2_CALLPEAK {
     input:
     tuple val(meta), path(ipbam), path(controlbam)
     val   macs2_gsize
-    
+
     output:
     tuple val(meta), path("*.{narrowPeak,broadPeak}"), emit: peak
     tuple val(meta), path("*.xls")                   , emit: xls
@@ -44,7 +44,7 @@ process MACS2_CALLPEAK {
         --format $format \\
         --name $prefix \\
         --treatment $ipbam \\
-         $control
+        $control
 
     macs2 --version | sed -e "s/macs2 //g" > ${software}.version.txt
     """

software/phantompeakqualtools/functions.nf

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

software/phantompeakqualtools/main.nf

@@ -19,10 +19,10 @@ process PHANTOMPEAKQUALTOOLS {
     } else {
         container "quay.io/biocontainers/phantompeakqualtools:1.2.2--0"
     }
-    
+
     input:
     tuple val(meta), path(bam)
-    
+
     output:
     tuple val(meta), path("*.out")  , emit: spp
     tuple val(meta), path("*.pdf")  , emit: pdf

software/picard/collectmultiplemetrics/functions.nf

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

software/picard/markduplicates/functions.nf

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

software/picard/markduplicates/main.nf

@@ -10,7 +10,7 @@ process PICARD_MARKDUPLICATES {
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-    
+
     conda (params.enable_conda ? "bioconda::picard=2.23.9" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://depot.galaxyproject.org/singularity/picard:2.23.9--0"
@@ -20,7 +20,7 @@ process PICARD_MARKDUPLICATES {
 
     input:
     tuple val(meta), path(bam)
-    
+
     output:
     tuple val(meta), path("*.bam")        , emit: bam
     tuple val(meta), path("*.metrics.txt"), emit: metrics

software/picard/mergesamfiles/functions.nf

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

software/picard/mergesamfiles/main.nf

@@ -20,7 +20,7 @@ process PICARD_MERGESAMFILES {
 
     input:
     tuple val(meta), path(bams)
- 
+
     output:
     tuple val(meta), path("*.bam"), emit: bam
     path  "*.version.txt"         , emit: version

software/preseq/lcextrap/functions.nf

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

software/preseq/lcextrap/main.nf

@@ -18,10 +18,10 @@ process PRESEQ_LCEXTRAP {
     } else {
         container "quay.io/biocontainers/preseq:2.0.3--hf53bd2b_3"
     }
-    
+
     input:
     tuple val(meta), path(bam)
-    
+
     output:
     tuple val(meta), path("*.ccurve.txt"), emit: ccurve
     tuple val(meta), path("*.log")       , emit: log

software/qualimap/rnaseq/functions.nf

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

software/qualimap/rnaseq/main.nf

@@ -21,7 +21,7 @@ process QUALIMAP_RNASEQ {
     input:
     tuple val(meta), path(bam)
     path  gtf
-    
+
     output:
     tuple val(meta), path("${prefix}"), emit: results
     path  "*.version.txt"             , emit: version

software/rsem/calculateexpression/functions.nf

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

software/rsem/calculateexpression/main.nf

@@ -1,61 +1,61 @@
-// Import generic module functions
+// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
-
+
-params.options = [:]
+params.options = [:]
-def options    = initOptions(params.options)
+def options    = initOptions(params.options)
-
+
-process RSEM_CALCULATEEXPRESSION {
+process RSEM_CALCULATEEXPRESSION {
-    tag "$meta.id"
+    tag "$meta.id"
-    label 'process_high'
+    label 'process_high'
-    publishDir "${params.outdir}",
+    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
+        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
+
-    conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
+    conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
-    } else {
+    } else {
-        container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
+        container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
-    }
+    }
-
+
-    input:
+    input:
-    tuple val(meta), path(reads)
+    tuple val(meta), path(reads)
-    path  index
+    path  index
-    
+
-    output:
+    output:
-    tuple val(meta), path("*.genes.results")   , emit: counts_gene
+    tuple val(meta), path("*.genes.results")   , emit: counts_gene
-    tuple val(meta), path("*.isoforms.results"), emit: counts_transcript
+    tuple val(meta), path("*.isoforms.results"), emit: counts_transcript
-    tuple val(meta), path("*.stat")            , emit: stat
+    tuple val(meta), path("*.stat")            , emit: stat
-    tuple val(meta), path("*.log")             , emit: logs
+    tuple val(meta), path("*.log")             , emit: logs
-    path  "*.version.txt"                      , emit: version
+    path  "*.version.txt"                      , emit: version
-
+
-    tuple val(meta), path("*.STAR.genome.bam")       , optional:true, emit: bam_star
+    tuple val(meta), path("*.STAR.genome.bam")       , optional:true, emit: bam_star
-    tuple val(meta), path("${prefix}.genome.bam")    , optional:true, emit: bam_genome
+    tuple val(meta), path("${prefix}.genome.bam")    , optional:true, emit: bam_genome
-    tuple val(meta), path("${prefix}.transcript.bam"), optional:true, emit: bam_transcript
+    tuple val(meta), path("${prefix}.transcript.bam"), optional:true, emit: bam_transcript
-
+
-    script:
+    script:
-    def software   = getSoftwareName(task.process)
+    def software   = getSoftwareName(task.process)
-    prefix         = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    prefix         = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-
+
-    def strandedness = ''
+    def strandedness = ''
-    if (meta.strandedness == 'forward') {
+    if (meta.strandedness == 'forward') {
-        strandedness = '--strandedness forward'
+        strandedness = '--strandedness forward'
-    } else if (meta.strandedness == 'reverse') {
+    } else if (meta.strandedness == 'reverse') {
-        strandedness = '--strandedness reverse'
+        strandedness = '--strandedness reverse'
-    }
+    }
-    def paired_end = meta.single_end ? "" : "--paired-end"
+    def paired_end = meta.single_end ? "" : "--paired-end"
-    """
+    """
-    INDEX=`find -L ./ -name "*.grp" | sed 's/.grp//'`
+    INDEX=`find -L ./ -name "*.grp" | sed 's/.grp//'`
-    rsem-calculate-expression \\
+    rsem-calculate-expression \\
-        --num-threads $task.cpus \\
+        --num-threads $task.cpus \\
-        --temporary-folder ./tmp/ \\
+        --temporary-folder ./tmp/ \\
-        $strandedness \\
+        $strandedness \\
-        $paired_end \\
+        $paired_end \\
-        $options.args \\
+        $options.args \\
-        $reads \\
+        $reads \\
-        \$INDEX \\
+        \$INDEX \\
-        $prefix
+        $prefix
-
+
-    rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g" > ${software}.version.txt
+    rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g" > ${software}.version.txt
-    """
+    """
-}
+}

software/rsem/preparereference/functions.nf

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

software/rsem/preparereference/main.nf

@@ -1,68 +1,68 @@
-// Import generic module functions
+// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
-
+
-params.options = [:]
+params.options = [:]
-def options    = initOptions(params.options)
+def options    = initOptions(params.options)
-
+
-process RSEM_PREPAREREFERENCE {
+process RSEM_PREPAREREFERENCE {
-    tag "$fasta"
+    tag "$fasta"
-    label 'process_high'
+    label 'process_high'
-    publishDir "${params.outdir}",
+    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
+        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
-
+
-    conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
+    conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
-    } else {
+    } else {
-        container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
+        container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
-    }
+    }
-
+
-    input:
+    input:
-    path fasta
+    path fasta
-    path gtf
+    path gtf
-    
+
-    output:
+    output:
-    path "rsem"         , emit: index
+    path "rsem"         , emit: index
-    path "*.version.txt", emit: version
+    path "*.version.txt", emit: version
-
+
-    script:
+    script:
-    def software = getSoftwareName(task.process)
+    def software = getSoftwareName(task.process)
-    def args     = options.args.tokenize()
+    def args     = options.args.tokenize()
-    if (args.contains('--star')) {
+    if (args.contains('--star')) {
-        args.removeIf { it.contains('--star') }
+        args.removeIf { it.contains('--star') }
-        def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
+        def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
-        """
+        """
-        mkdir rsem
+        mkdir rsem
-        STAR \\
+        STAR \\
-            --runMode genomeGenerate \\
+            --runMode genomeGenerate \\
-            --genomeDir rsem/ \\
+            --genomeDir rsem/ \\
-            --genomeFastaFiles $fasta \\
+            --genomeFastaFiles $fasta \\
-            --sjdbGTFfile $gtf \\
+            --sjdbGTFfile $gtf \\
-            --runThreadN $task.cpus \\
+            --runThreadN $task.cpus \\
-            $memory \\
+            $memory \\
-            $options.args2
+            $options.args2
-        
+
-        rsem-prepare-reference \\
+        rsem-prepare-reference \\
-            --gtf $gtf \\
+            --gtf $gtf \\
-            --num-threads $task.cpus \\
+            --num-threads $task.cpus \\
-            ${args.join(' ')} \\
+            ${args.join(' ')} \\
-            $fasta \\
+            $fasta \\
-            rsem/genome
+            rsem/genome
-
+
-        rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g" > ${software}.version.txt
+        rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g" > ${software}.version.txt
-        """
+        """
-    } else {
+    } else {
-        """
+        """
-        mkdir rsem
+        mkdir rsem
-        rsem-prepare-reference \\
+        rsem-prepare-reference \\
-            --gtf $gtf \\
+            --gtf $gtf \\
-            --num-threads $task.cpus \\
+            --num-threads $task.cpus \\
-            $options.args \\
+            $options.args \\
-            $fasta \\
+            $fasta \\
-            rsem/genome
+            rsem/genome
-
+
-        rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g" > ${software}.version.txt
+        rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g" > ${software}.version.txt
-        """
+        """
-    }
+    }
-}
+}

software/rseqc/bamstat/functions.nf

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

software/rseqc/bamstat/main.nf

@@ -1,39 +1,39 @@
-// Import generic module functions
+// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
-
+
-params.options = [:]
+params.options = [:]
-def options    = initOptions(params.options)
+def options    = initOptions(params.options)
-
+
-process RSEQC_BAMSTAT {
+process RSEQC_BAMSTAT {
-    tag "$meta.id"
+    tag "$meta.id"
-    label 'process_medium'
+    label 'process_medium'
-    publishDir "${params.outdir}",
+    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
+        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
+
-    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
-    } else {
+    } else {
-        container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+        container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
-    }
+    }
-
+
-    input:
+    input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bam)
-    
+
-    output:
+    output:
-    tuple val(meta), path("*.bam_stat.txt"), emit: txt
+    tuple val(meta), path("*.bam_stat.txt"), emit: txt
-    path  "*.version.txt"                  , emit: version
+    path  "*.version.txt"                  , emit: version
-
+
-    script:
+    script:
-    def software = getSoftwareName(task.process) 
+    def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    """
+    """
-    bam_stat.py \\
+    bam_stat.py \\
-        -i $bam \\
+        -i $bam \\
-        $options.args \\
+        $options.args \\
-        > ${prefix}.bam_stat.txt
+        > ${prefix}.bam_stat.txt
-
+
-    bam_stat.py --version | sed -e "s/bam_stat.py //g" > ${software}.version.txt
+    bam_stat.py --version | sed -e "s/bam_stat.py //g" > ${software}.version.txt
-    """
+    """
-}
+}

software/rseqc/inferexperiment/functions.nf

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

software/rseqc/inferexperiment/main.nf

@@ -1,41 +1,41 @@
-// Import generic module functions
+// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
-
+
-params.options = [:]
+params.options = [:]
-def options    = initOptions(params.options)
+def options    = initOptions(params.options)
-
+
-process RSEQC_INFEREXPERIMENT {
+process RSEQC_INFEREXPERIMENT {
-    tag "$meta.id"
+    tag "$meta.id"
-    label 'process_medium'
+    label 'process_medium'
-    publishDir "${params.outdir}",
+    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
+        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
+
-    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
-    } else {
+    } else {
-        container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+        container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
-    }
+    }
-
+
-    input:
+    input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bam)
-    path  bed
+    path  bed
-    
+
-    output:
+    output:
-    tuple val(meta), path("*.infer_experiment.txt"), emit: txt
+    tuple val(meta), path("*.infer_experiment.txt"), emit: txt
-    path  "*.version.txt"                          , emit: version
+    path  "*.version.txt"                          , emit: version
-
+
-    script:
+    script:
-    def software = getSoftwareName(task.process) 
+    def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    """
+    """
-    infer_experiment.py \\
+    infer_experiment.py \\
-        -i $bam \\
+        -i $bam \\
-        -r $bed \\
+        -r $bed \\
-        $options.args \\
+        $options.args \\
-        > ${prefix}.infer_experiment.txt
+        > ${prefix}.infer_experiment.txt
-
+
-    infer_experiment.py --version | sed -e "s/infer_experiment.py //g" > ${software}.version.txt
+    infer_experiment.py --version | sed -e "s/infer_experiment.py //g" > ${software}.version.txt
-    """
+    """
-}
+}

software/rseqc/innerdistance/functions.nf

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

software/rseqc/innerdistance/main.nf

@@ -1,53 +1,53 @@
-// Import generic module functions
+// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
-
+
-params.options = [:]
+params.options = [:]
-def options    = initOptions(params.options)
+def options    = initOptions(params.options)
-
+
-process RSEQC_INNERDISTANCE {
+process RSEQC_INNERDISTANCE {
-    tag "$meta.id"
+    tag "$meta.id"
-    label 'process_medium'
+    label 'process_medium'
-    publishDir "${params.outdir}",
+    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
+        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
+
-    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
-    } else {
+    } else {
-        container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+        container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
-    }
+    }
-
+
-    input:
+    input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bam)
-    path  bed
+    path  bed
-    
+
-    output:
+    output:
-    tuple val(meta), path("*distance.txt"), optional:true, emit: distance
+    tuple val(meta), path("*distance.txt"), optional:true, emit: distance
-    tuple val(meta), path("*freq.txt")    , optional:true, emit: freq
+    tuple val(meta), path("*freq.txt")    , optional:true, emit: freq
-    tuple val(meta), path("*mean.txt")    , optional:true, emit: mean
+    tuple val(meta), path("*mean.txt")    , optional:true, emit: mean
-    tuple val(meta), path("*.pdf")        , optional:true, emit: pdf
+    tuple val(meta), path("*.pdf")        , optional:true, emit: pdf
-    tuple val(meta), path("*.r")          , optional:true, emit: rscript
+    tuple val(meta), path("*.r")          , optional:true, emit: rscript
-    path  "*.version.txt"                 , emit: version
+    path  "*.version.txt"                 , emit: version
-
+
-    script:
+    script:
-    def software = getSoftwareName(task.process)
+    def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    if (!meta.single_end) {
+    if (!meta.single_end) {
-        """
+        """
-        inner_distance.py \\
+        inner_distance.py \\
-            -i $bam \\
+            -i $bam \\
-            -r $bed \\
+            -r $bed \\
-            -o $prefix \\
+            -o $prefix \\
-            $options.args \\
+            $options.args \\
-            > stdout.txt
+            > stdout.txt
-        head -n 2 stdout.txt > ${prefix}.inner_distance_mean.txt
+        head -n 2 stdout.txt > ${prefix}.inner_distance_mean.txt
-
+
-        inner_distance.py --version | sed -e "s/inner_distance.py //g" > ${software}.version.txt
+        inner_distance.py --version | sed -e "s/inner_distance.py //g" > ${software}.version.txt
-        """
+        """
-    } else {
+    } else {
-        """
+        """
-        inner_distance.py --version | sed -e "s/inner_distance.py //g" > ${software}.version.txt
+        inner_distance.py --version | sed -e "s/inner_distance.py //g" > ${software}.version.txt
-        """
+        """
-    }
+    }
-}
+}

software/rseqc/junctionannotation/functions.nf

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

software/rseqc/junctionannotation/main.nf

@@ -1,48 +1,48 @@
-// Import generic module functions
+// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
-
+
-params.options = [:]
+params.options = [:]
-def options    = initOptions(params.options)
+def options    = initOptions(params.options)
-
+
-process RSEQC_JUNCTIONANNOTATION {
+process RSEQC_JUNCTIONANNOTATION {
-    tag "$meta.id"
+    tag "$meta.id"
-    label 'process_medium'
+    label 'process_medium'
-    publishDir "${params.outdir}",
+    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
+        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
+
-    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
-    } else {
+    } else {
-        container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+        container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
-    }
+    }
-
+
-    input:
+    input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bam)
-    path  bed
+    path  bed
-    
+
-    output:
+    output:
-    tuple val(meta), path("*.junction.bed"), emit: bed
+    tuple val(meta), path("*.junction.bed"), emit: bed
-    tuple val(meta), path("*.Interact.bed"), emit: interact_bed
+    tuple val(meta), path("*.Interact.bed"), emit: interact_bed
-    tuple val(meta), path("*.xls")         , emit: xls
+    tuple val(meta), path("*.xls")         , emit: xls
-    tuple val(meta), path("*junction.pdf") , emit: pdf
+    tuple val(meta), path("*junction.pdf") , emit: pdf
-    tuple val(meta), path("*events.pdf")   , emit: events_pdf
+    tuple val(meta), path("*events.pdf")   , emit: events_pdf
-    tuple val(meta), path("*.r")           , emit: rscript
+    tuple val(meta), path("*.r")           , emit: rscript
-    tuple val(meta), path("*.log")         , emit: log
+    tuple val(meta), path("*.log")         , emit: log
-    path  "*.version.txt"                  , emit: version
+    path  "*.version.txt"                  , emit: version
-
+
-    script:
+    script:
-    def software = getSoftwareName(task.process)
+    def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    """
+    """
-    junction_annotation.py \\
+    junction_annotation.py \\
-        -i $bam \\
+        -i $bam \\
-        -r $bed \\
+        -r $bed \\
-        -o $prefix \\
+        -o $prefix \\
-        $options.args \\
+        $options.args \\
-        2> ${prefix}.junction_annotation.log
+        2> ${prefix}.junction_annotation.log
-
+
-    junction_annotation.py --version | sed -e "s/junction_annotation.py //g" > ${software}.version.txt
+    junction_annotation.py --version | sed -e "s/junction_annotation.py //g" > ${software}.version.txt
-    """
+    """
-}
+}

software/rseqc/junctionsaturation/functions.nf

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

software/rseqc/junctionsaturation/main.nf

@@ -1,42 +1,42 @@
-// Import generic module functions
+// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
-
+
-params.options = [:]
+params.options = [:]
-def options    = initOptions(params.options)
+def options    = initOptions(params.options)
-
+
-process RSEQC_JUNCTIONSATURATION {
+process RSEQC_JUNCTIONSATURATION {
-    tag "$meta.id"
+    tag "$meta.id"
-    label 'process_medium'
+    label 'process_medium'
-    publishDir "${params.outdir}",
+    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
+        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
+
-    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
-    } else {
+    } else {
-        container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+        container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
-    }
+    }
-
+
-    input:
+    input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bam)
-    path  bed
+    path  bed
-    
+
-    output:
+    output:
-    tuple val(meta), path("*.pdf"), emit: pdf
+    tuple val(meta), path("*.pdf"), emit: pdf
-    tuple val(meta), path("*.r")  , emit: rscript
+    tuple val(meta), path("*.r")  , emit: rscript
-    path  "*.version.txt"         , emit: version
+    path  "*.version.txt"         , emit: version
-
+
-    script:
+    script:
-    def software = getSoftwareName(task.process)
+    def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    """
+    """
-    junction_saturation.py \\
+    junction_saturation.py \\
-        -i $bam \\
+        -i $bam \\
-        -r $bed \\
+        -r $bed \\
-        -o $prefix \\
+        -o $prefix \\
-        $options.args
+        $options.args
-
+
-    junction_saturation.py --version | sed -e "s/junction_saturation.py //g" > ${software}.version.txt
+    junction_saturation.py --version | sed -e "s/junction_saturation.py //g" > ${software}.version.txt
-    """
+    """
-}
+}

software/rseqc/readdistribution/functions.nf

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

software/rseqc/readdistribution/main.nf

@@ -1,40 +1,40 @@
-// Import generic module functions
+// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
-
+
-params.options = [:]
+params.options = [:]
-def options    = initOptions(params.options)
+def options    = initOptions(params.options)
-
+
-process RSEQC_READDISTRIBUTION {
+process RSEQC_READDISTRIBUTION {
-    tag "$meta.id"
+    tag "$meta.id"
-    label 'process_medium'
+    label 'process_medium'
-    publishDir "${params.outdir}",
+    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
+        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
+
-    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
-    } else {
+    } else {
-        container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+        container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
-    }
+    }
-
+
-    input:
+    input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bam)
-    path  bed
+    path  bed
-    
+
-    output:
+    output:
-    tuple val(meta), path("*.read_distribution.txt"), emit: txt
+    tuple val(meta), path("*.read_distribution.txt"), emit: txt
-    path  "*.version.txt"                           , emit: version
+    path  "*.version.txt"                           , emit: version
-
+
-    script:
+    script:
-    def software = getSoftwareName(task.process)
+    def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    """
+    """
-    read_distribution.py \\
+    read_distribution.py \\
-        -i $bam \\
+        -i $bam \\
-        -r $bed \\
+        -r $bed \\
-         > ${prefix}.read_distribution.txt
+        > ${prefix}.read_distribution.txt
-
+
-    read_distribution.py --version | sed -e "s/read_distribution.py //g" > ${software}.version.txt
+    read_distribution.py --version | sed -e "s/read_distribution.py //g" > ${software}.version.txt
-    """
+    """
-}
+}

software/rseqc/readduplication/functions.nf

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

software/rseqc/readduplication/main.nf

@@ -1,42 +1,42 @@
-// Import generic module functions
+// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
-
+
-params.options = [:]
+params.options = [:]
-def options    = initOptions(params.options)
+def options    = initOptions(params.options)
-
+
-process RSEQC_READDUPLICATION {
+process RSEQC_READDUPLICATION {
-    tag "$meta.id"
+    tag "$meta.id"
-    label 'process_medium'
+    label 'process_medium'
-    publishDir "${params.outdir}",
+    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
+        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
+
-    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
-    } else {
+    } else {
-        container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+        container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
-    }
+    }
-
+
-    input:
+    input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bam)
-    
+
-    output:
+    output:
-    tuple val(meta), path("*seq.DupRate.xls"), emit: seq_xls
+    tuple val(meta), path("*seq.DupRate.xls"), emit: seq_xls
-    tuple val(meta), path("*pos.DupRate.xls"), emit: pos_xls
+    tuple val(meta), path("*pos.DupRate.xls"), emit: pos_xls
-    tuple val(meta), path("*.pdf")           , emit: pdf
+    tuple val(meta), path("*.pdf")           , emit: pdf
-    tuple val(meta), path("*.r")             , emit: rscript
+    tuple val(meta), path("*.r")             , emit: rscript
-    path  "*.version.txt"                    , emit: version
+    path  "*.version.txt"                    , emit: version
-
+
-    script:
+    script:
-    def software = getSoftwareName(task.process)
+    def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    """
+    """
-    read_duplication.py \\
+    read_duplication.py \\
-        -i $bam \\
+        -i $bam \\
-        -o $prefix \\
+        -o $prefix \\
-        $options.args
+        $options.args
-
+
-    read_duplication.py --version | sed -e "s/read_duplication.py //g" > ${software}.version.txt
+    read_duplication.py --version | sed -e "s/read_duplication.py //g" > ${software}.version.txt
-    """
+    """
-}
+}

software/salmon/index/functions.nf

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

software/salmon/index/main.nf

@@ -1,51 +1,51 @@
-// Import generic module functions
+// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
-
+
-params.options = [:]
+params.options = [:]
-def options    = initOptions(params.options)
+def options    = initOptions(params.options)
-
+
-process SALMON_INDEX {
+process SALMON_INDEX {
-    tag "$transcript_fasta"
+    tag "$transcript_fasta"
-    label "process_medium"
+    label "process_medium"
-    publishDir "${params.outdir}",
+    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
+        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
-
+
-    conda (params.enable_conda ? "bioconda::salmon=1.4.0" : null)
+    conda (params.enable_conda ? "bioconda::salmon=1.4.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/salmon:1.4.0--hf69c8f4_0"
+        container "https://depot.galaxyproject.org/singularity/salmon:1.4.0--hf69c8f4_0"
-    } else {
+    } else {
-        container "quay.io/biocontainers/salmon:1.4.0--hf69c8f4_0"
+        container "quay.io/biocontainers/salmon:1.4.0--hf69c8f4_0"
-    }
+    }
-
+
-    input:
+    input:
-    path genome_fasta
+    path genome_fasta
-    path transcript_fasta
+    path transcript_fasta
-
+
-    output:
+    output:
-    path "salmon"       , emit: index
+    path "salmon"       , emit: index
-    path "*.version.txt", emit: version
+    path "*.version.txt", emit: version
-
+
-    script:
+    script:
-    def software      = getSoftwareName(task.process)
+    def software      = getSoftwareName(task.process)
-    def get_decoy_ids = "grep '^>' $genome_fasta | cut -d ' ' -f 1 > decoys.txt"
+    def get_decoy_ids = "grep '^>' $genome_fasta | cut -d ' ' -f 1 > decoys.txt"
-    def gentrome      = "gentrome.fa"
+    def gentrome      = "gentrome.fa"
-    if (genome_fasta.endsWith('.gz')) {
+    if (genome_fasta.endsWith('.gz')) {
-        get_decoy_ids = "grep '^>' <(gunzip -c $genome_fasta) | cut -d ' ' -f 1 > decoys.txt"
+        get_decoy_ids = "grep '^>' <(gunzip -c $genome_fasta) | cut -d ' ' -f 1 > decoys.txt"
-        gentrome      = "gentrome.fa.gz"
+        gentrome      = "gentrome.fa.gz"
-    }
+    }
-    """
+    """
-    $get_decoy_ids
+    $get_decoy_ids
-    sed -i.bak -e 's/>//g' decoys.txt
+    sed -i.bak -e 's/>//g' decoys.txt
-    cat $transcript_fasta $genome_fasta > $gentrome
+    cat $transcript_fasta $genome_fasta > $gentrome
-
+
-    salmon \\
+    salmon \\
-        index \\
+        index \\
-        --threads $task.cpus \\
+        --threads $task.cpus \\
-        -t $gentrome \\
+        -t $gentrome \\
-        -d decoys.txt \\
+        -d decoys.txt \\
-        $options.args \\
+        $options.args \\
-        -i salmon
+        -i salmon
-    salmon --version | sed -e "s/salmon //g" > ${software}.version.txt
+    salmon --version | sed -e "s/salmon //g" > ${software}.version.txt
-    """
+    """
-}
+}

software/salmon/quant/functions.nf

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

software/salmon/quant/main.nf

@@ -24,7 +24,7 @@ process SALMON_QUANT {
     path  gtf
     path  transcript_fasta
     val   alignment_mode
-    
+
     output:
     tuple val(meta), path("${prefix}"), emit: results
     path  "*.version.txt"             , emit: version
@@ -39,7 +39,7 @@ process SALMON_QUANT {
         reference   = "-t $transcript_fasta"
         input_reads = "-a $reads"
     }
-    
+
     def strandedness = meta.single_end ? 'U' : 'IU'
     if (meta.strandedness == 'forward') {
         strandedness = meta.single_end ? 'SF' : 'ISF'

software/samtools/flagstat/functions.nf

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

software/samtools/flagstat/main.nf

@@ -1,32 +1,32 @@
-// Import generic module functions
+// Import generic module functions
-include { saveFiles; getSoftwareName } from './functions'
+include { saveFiles; getSoftwareName } from './functions'
-
+
-params.options = [:]
+params.options = [:]
-
+
-process SAMTOOLS_FLAGSTAT {
+process SAMTOOLS_FLAGSTAT {
-    tag "$meta.id"
+    tag "$meta.id"
-    publishDir "${params.outdir}",
+    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
+        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
+
-    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
-    } else {
+    } else {
-        container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+        container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
-    }
+    }
-
+
-    input:
+    input:
-    tuple val(meta), path(bam), path(bai)
+    tuple val(meta), path(bam), path(bai)
-    
+
-    output:
+    output:
-    tuple val(meta), path("*.flagstat"), emit: flagstat
+    tuple val(meta), path("*.flagstat"), emit: flagstat
-    path  "*.version.txt"              , emit: version
+    path  "*.version.txt"              , emit: version
-
+
-    script:
+    script:
-    def software = getSoftwareName(task.process)
+    def software = getSoftwareName(task.process)
-    """
+    """
-    samtools flagstat $bam > ${bam}.flagstat
+    samtools flagstat $bam > ${bam}.flagstat
-    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
+    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
-    """
+    """
-}
+}

software/samtools/idxstats/functions.nf

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

software/samtools/idxstats/main.nf

@@ -1,32 +1,32 @@
-// Import generic module functions
+// Import generic module functions
-include { saveFiles; getSoftwareName } from './functions'
+include { saveFiles; getSoftwareName } from './functions'
-
+
-params.options = [:]
+params.options = [:]
-
+
-process SAMTOOLS_IDXSTATS {
+process SAMTOOLS_IDXSTATS {
-    tag "$meta.id"
+    tag "$meta.id"
-    publishDir "${params.outdir}",
+    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
+        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
+
-    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
-    } else {
+    } else {
-        container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+        container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
-    }
+    }
-
+
-    input:
+    input:
-    tuple val(meta), path(bam), path(bai)
+    tuple val(meta), path(bam), path(bai)
-    
+
-    output:
+    output:
-    tuple val(meta), path("*.idxstats"), emit: idxstats
+    tuple val(meta), path("*.idxstats"), emit: idxstats
-    path  "*.version.txt"              , emit: version
+    path  "*.version.txt"              , emit: version
-
+
-    script:
+    script:
-    def software = getSoftwareName(task.process)
+    def software = getSoftwareName(task.process)
-    """
+    """
-    samtools idxstats $bam > ${bam}.idxstats
+    samtools idxstats $bam > ${bam}.idxstats
-    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
+    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
-    """
+    """
-}
+}

software/samtools/index/functions.nf

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

software/samtools/index/main.nf

@@ -1,32 +1,32 @@
-// Import generic module functions
+// Import generic module functions
-include { saveFiles; getSoftwareName } from './functions'
+include { saveFiles; getSoftwareName } from './functions'
-
+
-params.options = [:]
+params.options = [:]
-
+
-process SAMTOOLS_INDEX {
+process SAMTOOLS_INDEX {
-    tag "$meta.id"
+    tag "$meta.id"
-    publishDir "${params.outdir}",
+    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
+        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
+
-    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
-    } else {
+    } else {
-        container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+        container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
-    }
+    }
-
+
-    input:
+    input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bam)
-    
+
-    output:
+    output:
-    tuple val(meta), path("*.bai"), emit: bai
+    tuple val(meta), path("*.bai"), emit: bai
-    path  "*.version.txt"         , emit: version
+    path  "*.version.txt"         , emit: version
-
+
-    script:
+    script:
-    def software = getSoftwareName(task.process)
+    def software = getSoftwareName(task.process)
-    """
+    """
-    samtools index $bam
+    samtools index $bam
-    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
+    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
-    """
+    """
-}
+}

software/samtools/sort/functions.nf

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

software/samtools/sort/main.nf

@@ -1,35 +1,35 @@
-// Import generic module functions
+// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
-
+
-params.options = [:]
+params.options = [:]
-def options    = initOptions(params.options)
+def options    = initOptions(params.options)
-
+
-process SAMTOOLS_SORT {
+process SAMTOOLS_SORT {
-    tag "$meta.id"
+    tag "$meta.id"
-    label 'process_medium'
+    label 'process_medium'
-    publishDir "${params.outdir}",
+    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
+        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
+
-    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
-    } else {
+    } else {
-        container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+        container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
-    }
+    }
-
+
-    input:
+    input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bam)
-    
+
-    output:
+    output:
-    tuple val(meta), path("*.bam"), emit: bam
+    tuple val(meta), path("*.bam"), emit: bam
-    path  "*.version.txt"         , emit: version
+    path  "*.version.txt"         , emit: version
-
+
-    script:
+    script:
-    def software = getSoftwareName(task.process)
+    def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    """
+    """
-    samtools sort $options.args -@ $task.cpus -o ${prefix}.bam -T $prefix $bam
+    samtools sort $options.args -@ $task.cpus -o ${prefix}.bam -T $prefix $bam
-    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
+    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
-    """
+    """
-}
+}

software/samtools/stats/functions.nf

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

software/samtools/stats/main.nf

@@ -1,32 +1,32 @@
-// Import generic module functions
+// Import generic module functions
-include { saveFiles; getSoftwareName } from './functions'
+include { saveFiles; getSoftwareName } from './functions'
-
+
-params.options = [:]
+params.options = [:]
-
+
-process SAMTOOLS_STATS {
+process SAMTOOLS_STATS {
-    tag "$meta.id"
+    tag "$meta.id"
-    publishDir "${params.outdir}",
+    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
+        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
+
-    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
-    } else {
+    } else {
-        container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+        container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
-    }
+    }
-    
+
-    input:
+    input:
-    tuple val(meta), path(bam), path(bai)
+    tuple val(meta), path(bam), path(bai)
-    
+
-    output:
+    output:
-    tuple val(meta), path("*.stats"), emit: stats
+    tuple val(meta), path("*.stats"), emit: stats
-    path  "*.version.txt"           , emit: version
+    path  "*.version.txt"           , emit: version
-
+
-    script:
+    script:
-    def software = getSoftwareName(task.process)
+    def software = getSoftwareName(task.process)
-    """
+    """
-    samtools stats $bam > ${bam}.stats
+    samtools stats $bam > ${bam}.stats
-    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
+    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
-    """
+    """
-}
+}

software/sortmerna/functions.nf

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

software/sortmerna/main.nf

@@ -1,73 +1,73 @@
-// Import generic module functions
+// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
-
+
-params.options = [:]
+params.options = [:]
-def options    = initOptions(params.options)
+def options    = initOptions(params.options)
-
+
-process SORTMERNA {
+process SORTMERNA {
-    tag "$meta.id"
+    tag "$meta.id"
-    label "process_high"
+    label "process_high"
-    publishDir "${params.outdir}",
+    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
+        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
+
-    conda (params.enable_conda ? "bioconda::sortmerna=4.2.0" : null)
+    conda (params.enable_conda ? "bioconda::sortmerna=4.2.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/sortmerna:4.2.0--0"
+        container "https://depot.galaxyproject.org/singularity/sortmerna:4.2.0--0"
-    } else {
+    } else {
-        container "quay.io/biocontainers/sortmerna:4.2.0--0"
+        container "quay.io/biocontainers/sortmerna:4.2.0--0"
-    }
+    }
-    
+
-    input:
+    input:
-    tuple val(meta), path(reads)
+    tuple val(meta), path(reads)
-    path  fasta
+    path  fasta
-    
+
-    output:
+    output:
-    tuple val(meta), path("*.fastq.gz"), emit: reads
+    tuple val(meta), path("*.fastq.gz"), emit: reads
-    tuple val(meta), path("*.log")     , emit: log
+    tuple val(meta), path("*.log")     , emit: log
-    path  "*.version.txt"              , emit: version
+    path  "*.version.txt"              , emit: version
-
+
-    script:
+    script:
-    def software = getSoftwareName(task.process)
+    def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-
+
-    def Refs = ""
+    def Refs = ""
-    for (i=0; i<fasta.size(); i++) { Refs+= " --ref ${fasta[i]}" }
+    for (i=0; i<fasta.size(); i++) { Refs+= " --ref ${fasta[i]}" }
-    if (meta.single_end) {
+    if (meta.single_end) {
-        """
+        """
-        sortmerna \\
+        sortmerna \\
-            $Refs \\
+            $Refs \\
-            --reads $reads \\
+            --reads $reads \\
-            --threads $task.cpus \\
+            --threads $task.cpus \\
-            --workdir . \\
+            --workdir . \\
-            --aligned rRNA_reads \\
+            --aligned rRNA_reads \\
-            --other non_rRNA_reads \\
+            --other non_rRNA_reads \\
-            $options.args
+            $options.args
-
+
-        gzip -f < non_rRNA_reads.fq > ${prefix}.fastq.gz
+        gzip -f < non_rRNA_reads.fq > ${prefix}.fastq.gz
-        mv rRNA_reads.log ${prefix}.sortmerna.log
+        mv rRNA_reads.log ${prefix}.sortmerna.log
-
+
-        echo \$(sortmerna --version 2>&1) | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//' > ${software}.version.txt
+        echo \$(sortmerna --version 2>&1) | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//' > ${software}.version.txt
-        """
+        """
-    } else {
+    } else {
-        """
+        """
-        sortmerna \\
+        sortmerna \\
-            $Refs \\
+            $Refs \\
-            --reads ${reads[0]} \\
+            --reads ${reads[0]} \\
-            --reads ${reads[1]} \\
+            --reads ${reads[1]} \\
-            --threads $task.cpus \\
+            --threads $task.cpus \\
-            --workdir . \\
+            --workdir . \\
-            --aligned rRNA_reads \\
+            --aligned rRNA_reads \\
-            --other non_rRNA_reads \\
+            --other non_rRNA_reads \\
-            --paired_in \\
+            --paired_in \\
-            --out2 \\
+            --out2 \\
-            $options.args
+            $options.args
-
+
-        gzip -f < non_rRNA_reads_fwd.fq > ${prefix}_1.fastq.gz
+        gzip -f < non_rRNA_reads_fwd.fq > ${prefix}_1.fastq.gz
-        gzip -f < non_rRNA_reads_rev.fq > ${prefix}_2.fastq.gz
+        gzip -f < non_rRNA_reads_rev.fq > ${prefix}_2.fastq.gz
-        mv rRNA_reads.log ${prefix}.sortmerna.log
+        mv rRNA_reads.log ${prefix}.sortmerna.log
-
+
-        echo \$(sortmerna --version 2>&1) | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//' > ${software}.version.txt
+        echo \$(sortmerna --version 2>&1) | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//' > ${software}.version.txt
-        """
+        """
-    }
+    }
-}
+}

software/star/align/functions.nf

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

software/star/align/main.nf

@@ -1,66 +1,66 @@
-// Import generic module functions
+// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
-
+
-params.options = [:]
+params.options = [:]
-def options    = initOptions(params.options)
+def options    = initOptions(params.options)
-
+
-process STAR_ALIGN {
+process STAR_ALIGN {
-    tag "$meta.id"
+    tag "$meta.id"
-    label 'process_high'
+    label 'process_high'
-    publishDir "${params.outdir}",
+    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
+        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
+
-    // Note: 2.7X indices incompatible with AWS iGenomes.
+    // Note: 2.7X indices incompatible with AWS iGenomes.
-    conda (params.enable_conda ? "bioconda::star=2.6.1d" : null)
+    conda (params.enable_conda ? "bioconda::star=2.6.1d" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/star:2.6.1d--0"
+        container "https://depot.galaxyproject.org/singularity/star:2.6.1d--0"
-    } else {
+    } else {
-        container "quay.io/biocontainers/star:2.6.1d--0"
+        container "quay.io/biocontainers/star:2.6.1d--0"
-    }
+    }
-
+
-
+
-    input:
+    input:
-    tuple val(meta), path(reads)
+    tuple val(meta), path(reads)
-    path  index
+    path  index
-    path  gtf
+    path  gtf
-    
+
-    output:
+    output:
-    tuple val(meta), path("*Aligned.out.bam") , emit: bam
+    tuple val(meta), path("*Aligned.out.bam") , emit: bam
-    tuple val(meta), path("*Log.final.out")   , emit: log_final
+    tuple val(meta), path("*Log.final.out")   , emit: log_final
-    tuple val(meta), path("*Log.out")         , emit: log_out
+    tuple val(meta), path("*Log.out")         , emit: log_out
-    tuple val(meta), path("*Log.progress.out"), emit: log_progress
+    tuple val(meta), path("*Log.progress.out"), emit: log_progress
-    path  "*.version.txt"                     , emit: version
+    path  "*.version.txt"                     , emit: version
-
+
-    tuple val(meta), path("*sortedByCoord.out.bam")  , optional:true, emit: bam_sorted
+    tuple val(meta), path("*sortedByCoord.out.bam")  , optional:true, emit: bam_sorted
-    tuple val(meta), path("*toTranscriptome.out.bam"), optional:true, emit: bam_transcript
+    tuple val(meta), path("*toTranscriptome.out.bam"), optional:true, emit: bam_transcript
-    tuple val(meta), path("*fastq.gz")               , optional:true, emit: fastq
+    tuple val(meta), path("*fastq.gz")               , optional:true, emit: fastq
-    tuple val(meta), path("*.tab")                   , optional:true, emit: tab
+    tuple val(meta), path("*.tab")                   , optional:true, emit: tab
-
+
-    script:
+    script:
-    def software   = getSoftwareName(task.process)
+    def software   = getSoftwareName(task.process)
-    def prefix     = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def prefix     = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def ignore_gtf = params.star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf"
+    def ignore_gtf = params.star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf"
-    def seq_center = params.seq_center ? "--outSAMattrRGline ID:$prefix 'CN:$params.seq_center' 'SM:$prefix'" : "--outSAMattrRGline ID:$prefix 'SM:$prefix'"
+    def seq_center = params.seq_center ? "--outSAMattrRGline ID:$prefix 'CN:$params.seq_center' 'SM:$prefix'" : "--outSAMattrRGline ID:$prefix 'SM:$prefix'"
-    """
+    """
-    STAR \\
+    STAR \\
-        --genomeDir $index \\
+        --genomeDir $index \\
-        --readFilesIn $reads  \\
+        --readFilesIn $reads  \\
-        --runThreadN $task.cpus \\
+        --runThreadN $task.cpus \\
-        --outFileNamePrefix $prefix. \\
+        --outFileNamePrefix $prefix. \\
-        $ignore_gtf \\
+        $ignore_gtf \\
-        $seq_center \\
+        $seq_center \\
-        $options.args
+        $options.args
-
+
-    if [ -f ${prefix}.Unmapped.out.mate1 ]; then
+    if [ -f ${prefix}.Unmapped.out.mate1 ]; then
-        mv ${prefix}.Unmapped.out.mate1 ${prefix}.unmapped_1.fastq
+        mv ${prefix}.Unmapped.out.mate1 ${prefix}.unmapped_1.fastq
-        gzip ${prefix}.unmapped_1.fastq
+        gzip ${prefix}.unmapped_1.fastq
-    fi
+    fi
-    if [ -f ${prefix}.Unmapped.out.mate2 ]; then
+    if [ -f ${prefix}.Unmapped.out.mate2 ]; then
-        mv ${prefix}.Unmapped.out.mate2 ${prefix}.unmapped_2.fastq
+        mv ${prefix}.Unmapped.out.mate2 ${prefix}.unmapped_2.fastq
-        gzip ${prefix}.unmapped_2.fastq
+        gzip ${prefix}.unmapped_2.fastq
-    fi
+    fi
-
+
-    STAR --version | sed -e "s/STAR_//g" > ${software}.version.txt
+    STAR --version | sed -e "s/STAR_//g" > ${software}.version.txt
-    """
+    """
-}
+}

software/star/genomegenerate/functions.nf

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

software/stringtie/functions.nf

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

software/stringtie/main.nf

@@ -1,55 +1,55 @@
-// Import generic module functions
+// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
-
+
-params.options = [:]
+params.options = [:]
-def options    = initOptions(params.options)
+def options    = initOptions(params.options)
-
+
-process STRINGTIE {
+process STRINGTIE {
-    tag "$meta.id"
+    tag "$meta.id"
-    label 'process_medium'
+    label 'process_medium'
-    publishDir "${params.outdir}",
+    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
+        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
+
-    conda (params.enable_conda ? "bioconda::stringtie=2.1.4" : null)
+    conda (params.enable_conda ? "bioconda::stringtie=2.1.4" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/stringtie:2.1.4--h7e0af3c_0"
+        container "https://depot.galaxyproject.org/singularity/stringtie:2.1.4--h7e0af3c_0"
-    } else {
+    } else {
-        container "quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0"
+        container "quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0"
-    }
+    }
-
+
-    input:
+    input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bam)
-    path  gtf
+    path  gtf
-    
+
-    output:
+    output:
-    tuple val(meta), path("*.coverage.gtf")   , emit: coverage_gtf
+    tuple val(meta), path("*.coverage.gtf")   , emit: coverage_gtf
-    tuple val(meta), path("*.transcripts.gtf"), emit: transcript_gtf
+    tuple val(meta), path("*.transcripts.gtf"), emit: transcript_gtf
-    tuple val(meta), path("*.txt")            , emit: abundance
+    tuple val(meta), path("*.txt")            , emit: abundance
-    tuple val(meta), path("*.ballgown")       , emit: ballgown
+    tuple val(meta), path("*.ballgown")       , emit: ballgown
-    path  "*.version.txt"                     , emit: version
+    path  "*.version.txt"                     , emit: version
-
+
-    script:
+    script:
-    def software = getSoftwareName(task.process)
+    def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-
+
-    def strandedness = ''
+    def strandedness = ''
-    if (meta.strandedness == 'forward') {
+    if (meta.strandedness == 'forward') {
-        strandedness = '--fr'
+        strandedness = '--fr'
-    } else if (meta.strandedness == 'reverse') {
+    } else if (meta.strandedness == 'reverse') {
-        strandedness = '--rf'
+        strandedness = '--rf'
-    }
+    }
-    """
+    """
-    stringtie \\
+    stringtie \\
-        $bam \\
+        $bam \\
-        $strandedness \\
+        $strandedness \\
-        -G $gtf \\
+        -G $gtf \\
-        -o ${prefix}.transcripts.gtf \\
+        -o ${prefix}.transcripts.gtf \\
-        -A ${prefix}.gene_abundance.txt \\
+        -A ${prefix}.gene_abundance.txt \\
-        -C ${prefix}.coverage.gtf \\
+        -C ${prefix}.coverage.gtf \\
-        -b ${prefix}.ballgown \\
+        -b ${prefix}.ballgown \\
-        $options.args
+        $options.args
-
+
-    stringtie --version > ${software}.version.txt
+    stringtie --version > ${software}.version.txt
-    """
+    """
-}
+}

software/subread/featurecounts/functions.nf

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

software/subread/featurecounts/main.nf

@@ -20,7 +20,7 @@ process SUBREAD_FEATURECOUNTS {
 
     input:
     tuple val(meta), path(bams), path(annotation)
-    
+
     output:
     tuple val(meta), path("*featureCounts.txt")        , emit: counts
     tuple val(meta), path("*featureCounts.txt.summary"), emit: summary

software/trimgalore/functions.nf

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

software/ucsc/bedgraphtobigwig/functions.nf

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

software/ucsc/bedgraphtobigwig/main.nf

@@ -19,11 +19,11 @@ process UCSC_BEDGRAPHTOBIGWIG {
     } else {
         container "quay.io/biocontainers/ucsc-bedgraphtobigwig:377--h446ed27_1"
     }
-    
+
     input:
     tuple val(meta), path(bedgraph)
     path  sizes
-    
+
     output:
     tuple val(meta), path("*.bigWig"), emit: bigwig
     path "*.version.txt"             , emit: version

software/umitools/dedup/functions.nf

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

software/umitools/dedup/main.nf

@@ -1,41 +1,41 @@
-// Import generic module functions
+// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
-
+
-params.options = [:]
+params.options = [:]
-def options    = initOptions(params.options)
+def options    = initOptions(params.options)
-
+
-process UMITOOLS_DEDUP {
+process UMITOOLS_DEDUP {
-    tag "$meta.id"
+    tag "$meta.id"
-    label "process_medium"
+    label "process_medium"
-    publishDir "${params.outdir}",
+    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
+        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
+
-    conda (params.enable_conda ? "bioconda::umi_tools=1.1.1" : null)
+    conda (params.enable_conda ? "bioconda::umi_tools=1.1.1" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/umi_tools:1.1.1--py38h0213d0e_1"
+        container "https://depot.galaxyproject.org/singularity/umi_tools:1.1.1--py38h0213d0e_1"
-    } else {
+    } else {
-        container "quay.io/biocontainers/umi_tools:1.1.1--py38h0213d0e_1"
+        container "quay.io/biocontainers/umi_tools:1.1.1--py38h0213d0e_1"
-    }
+    }
-
+
-    input:
+    input:
-    tuple val(meta), path(bam), path(bai)
+    tuple val(meta), path(bam), path(bai)
-    
+
-    output:
+    output:
-    tuple val(meta), path("*.bam"), emit: bam
+    tuple val(meta), path("*.bam"), emit: bam
-    tuple val(meta), path("*.tsv"), emit: tsv
+    tuple val(meta), path("*.tsv"), emit: tsv
-    path  "*.version.txt"         , emit: version
+    path  "*.version.txt"         , emit: version
-
+
-    script:
+    script:
-    def software = getSoftwareName(task.process)
+    def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    """
+    """
-    umi_tools dedup \\
+    umi_tools dedup \\
-        -I $bam \\
+        -I $bam \\
-        -S ${prefix}.bam \\
+        -S ${prefix}.bam \\
-        --output-stats=$prefix \\
+        --output-stats=$prefix \\
-        $options.args \\
+        $options.args \\
-
+
-    umi_tools --version | sed -e "s/UMI-tools version: //g" > ${software}.version.txt
+    umi_tools --version | sed -e "s/UMI-tools version: //g" > ${software}.version.txt
-    """
+    """
-}
+}

software/umitools/extract/functions.nf

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

software/umitools/extract/main.nf

@@ -1,57 +1,57 @@
-// Import generic module functions
+// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
-
+
-params.options = [:]
+params.options = [:]
-def options    = initOptions(params.options)
+def options    = initOptions(params.options)
-
+
-process UMITOOLS_EXTRACT {
+process UMITOOLS_EXTRACT {
-    tag "$meta.id"
+    tag "$meta.id"
-    label "process_low"
+    label "process_low"
-    publishDir "${params.outdir}",
+    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
+        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
+
-    conda (params.enable_conda ? "bioconda::umi_tools=1.1.1" : null)
+    conda (params.enable_conda ? "bioconda::umi_tools=1.1.1" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/umi_tools:1.1.1--py38h0213d0e_1"
+        container "https://depot.galaxyproject.org/singularity/umi_tools:1.1.1--py38h0213d0e_1"
-    } else {
+    } else {
-        container "quay.io/biocontainers/umi_tools:1.1.1--py38h0213d0e_1"
+        container "quay.io/biocontainers/umi_tools:1.1.1--py38h0213d0e_1"
-    }
+    }
-
+
-    input:
+    input:
-    tuple val(meta), path(reads)
+    tuple val(meta), path(reads)
-
+
-    output:
+    output:
-    tuple val(meta), path("*.fastq.gz"), emit: reads
+    tuple val(meta), path("*.fastq.gz"), emit: reads
-    tuple val(meta), path("*.log")     , emit: log
+    tuple val(meta), path("*.log")     , emit: log
-    path  "*.version.txt"              , emit: version
+    path  "*.version.txt"              , emit: version
-
+
-    script:
+    script:
-    def software = getSoftwareName(task.process)
+    def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    if (meta.single_end) {
+    if (meta.single_end) {
-        """
+        """
-        umi_tools \\
+        umi_tools \\
-            extract \\
+            extract \\
-            -I $reads \\
+            -I $reads \\
-            -S ${prefix}.umi_extract.fastq.gz \\
+            -S ${prefix}.umi_extract.fastq.gz \\
-            $options.args \\
+            $options.args \\
-            > ${prefix}.umi_extract.log
+            > ${prefix}.umi_extract.log
-
+
-        umi_tools --version | sed -e "s/UMI-tools version: //g" > ${software}.version.txt
+        umi_tools --version | sed -e "s/UMI-tools version: //g" > ${software}.version.txt
-        """
+        """
-    }  else {
+    }  else {
-        """
+        """
-        umi_tools \\
+        umi_tools \\
-            extract \\
+            extract \\
-            -I ${reads[0]} \\
+            -I ${reads[0]} \\
-            --read2-in=${reads[1]} \\
+            --read2-in=${reads[1]} \\
-            -S ${prefix}.umi_extract_1.fastq.gz \\
+            -S ${prefix}.umi_extract_1.fastq.gz \\
-            --read2-out=${prefix}.umi_extract_2.fastq.gz \\
+            --read2-out=${prefix}.umi_extract_2.fastq.gz \\
-            $options.args \\
+            $options.args \\
-            > ${prefix}.umi_extract.log
+            > ${prefix}.umi_extract.log
-
+
-        umi_tools --version | sed -e "s/UMI-tools version: //g" > ${software}.version.txt
+        umi_tools --version | sed -e "s/UMI-tools version: //g" > ${software}.version.txt
-        """
+        """
-    }
+    }
-}
+}

tests/software/bowtie/main.nf

@@ -0,0 +1,33 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BOWTIE_INDEX } from '../../../software/bowtie/index/main.nf' addParams( options: [:] )
+include { BOWTIE_ALIGN } from '../../../software/bowtie/align/main.nf'  addParams( options: [:] )
+
+workflow test_bowtie_index {
+    fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    BOWTIE_INDEX ( fasta ) 
+}
+
+workflow test_bowtie_alignment_single_end {
+
+    fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    BOWTIE_INDEX ( fasta ) 
+
+    def input = []
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ]
+    BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
+}
+
+workflow test_bowtie_alignment_paired_end {
+    fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    BOWTIE_INDEX ( fasta ) 
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
+                file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
+    BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
+}

tests/software/bowtie/test.yml

@@ -0,0 +1,64 @@
+- name: Run bowtie index
+  command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_index -c tests/config/nextflow.config
+  tags:
+    - bowtie
+    - bowtie_index
+  files:
+    - path: output/bowtie/bowtie/NC_010473.1.ebwt
+      md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
+    - path: output/bowtie/bowtie/NC_010473.2.ebwt
+      md5sum: bfd10c5319c6a0dbc540fd789254a5dd
+    - path: output/bowtie/bowtie/NC_010473.3.ebwt
+      md5sum: cd201e81724f3099131aec16ef2cc53b
+    - path: output/bowtie/bowtie/NC_010473.4.ebwt
+      md5sum: bbb9d6d21ad765d135f95290204e8433
+    - path: output/bowtie/bowtie/NC_010473.rev.1.ebwt
+      md5sum: 44f719c2fe42e1f35d54e798775846d1
+    - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
+      md5sum: f3c398bba5158f4039334a932d79c051
+
+- name: Run bowtie index and align single-end
+  command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config
+  tags:
+    - bowtie
+    - bowtie_align
+  files:
+    - path: output/bowtie/bowtie/NC_010473.1.ebwt
+      md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
+    - path: output/bowtie/bowtie/NC_010473.2.ebwt
+      md5sum: bfd10c5319c6a0dbc540fd789254a5dd
+    - path: output/bowtie/bowtie/NC_010473.3.ebwt
+      md5sum: cd201e81724f3099131aec16ef2cc53b
+    - path: output/bowtie/bowtie/NC_010473.4.ebwt
+      md5sum: bbb9d6d21ad765d135f95290204e8433
+    - path: output/bowtie/bowtie/NC_010473.rev.1.ebwt
+      md5sum: 44f719c2fe42e1f35d54e798775846d1
+    - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
+      md5sum: f3c398bba5158f4039334a932d79c051
+    - path: output/bowtie/test.out
+      md5sum: a81cb18024616415a6cec3108a36fccd
+    - path: output/bowtie/test.bam
+      md5sum: 9feed8a55d4b5e600dcc577768ef07fc
+
+- name: Run bowtie index and align paired-end
+  command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_paired_end -c tests/config/nextflow.config
+  tags:
+    - bowtie
+    - bowtie_align
+  files:
+    - path: output/bowtie/bowtie/NC_010473.1.ebwt
+      md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
+    - path: output/bowtie/bowtie/NC_010473.2.ebwt
+      md5sum: bfd10c5319c6a0dbc540fd789254a5dd
+    - path: output/bowtie/bowtie/NC_010473.3.ebwt
+      md5sum: cd201e81724f3099131aec16ef2cc53b
+    - path: output/bowtie/bowtie/NC_010473.4.ebwt
+      md5sum: bbb9d6d21ad765d135f95290204e8433
+    - path: output/bowtie/bowtie/NC_010473.rev.1.ebwt
+      md5sum: 44f719c2fe42e1f35d54e798775846d1
+    - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
+      md5sum: f3c398bba5158f4039334a932d79c051
+    - path: output/bowtie/test.out
+      md5sum: a23e9a2a76e949aeb3693bcfae41a615
+    - path: output/bowtie/test.bam
+      md5sum: cf6a6381aa504e8342638ff3b509721e