Merge remote-tracking branch 'upstream/master' into bcftools_viralrecon

.github/workflows/bowtie2_align.yml

@@ -0,0 +1,42 @@
+name: bowtie2_align
+on:
+    push:
+        paths:
+            - software/bowtie2/align/**
+            - software/bowtie2/build/**
+            - .github/workflows/bowtie2_align.yml
+            - tests/software/bowtie2/**
+    pull_request:
+        paths:
+            - software/bowtie2/align/**
+            - software/bowtie2/build/**
+            - .github/workflows/bowtie2_align.yml
+            - tests/software/bowtie2/**
+
+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 bowtie2_align --symlink --wt 2

.github/workflows/bowtie2_build.yml

@@ -0,0 +1,40 @@
+name: bowtie2_build
+on:
+  push:
+    paths:
+      - software/bowtie2/build/**
+      - .github/workflows/bowtie2_build.yml
+      - tests/software/bowtie2/**
+  pull_request:
+    paths:
+      - software/bowtie2/build/**
+      - .github/workflows/bowtie2_build.yml
+      - tests/software/bowtie2/**
+
+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 bowtie2_build --symlink --wt 2

.github/workflows/bowtie_build.yml

@@ -1,14 +1,14 @@
-name: bowtie_index
+name: bowtie_build
 on:
   push:
     paths:
-      - software/bowtie/index/**
-      - .github/workflows/bowtie_index.yml
+      - software/bowtie/build/**
+      - .github/workflows/bowtie_build.yml
       - tests/software/bowtie/**
   pull_request:
     paths:
-      - software/bowtie/index/**
-      - .github/workflows/bowtie_index.yml
+      - software/bowtie/build/**
+      - .github/workflows/bowtie_build.yml
       - tests/software/bowtie/**
 
 jobs:
@@ -37,4 +37,4 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag bowtie_index --symlink --wt 2
+      - run: pytest --tag bowtie_build --symlink --wt 2

.github/workflows/fastp.yml

@@ -0,0 +1,40 @@
+name: fastp
+on:
+  push:
+    paths:
+      - software/fastp/**
+      - .github/workflows/fastp.yml
+      - tests
+  pull_request:
+    paths:
+      - software/fastp/**
+      - .github/workflows/fastp.yml
+      - tests
+
+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 fastp --symlink --wt 2

.github/workflows/quast.yml

@@ -0,0 +1,40 @@
+name: quast
+on:
+  push:
+    paths:
+      - software/quast/**
+      - .github/workflows/quast.yml
+      - tests
+  pull_request:
+    paths:
+      - software/pquast/**
+      - .github/workflows/quest.yml
+      - tests
+
+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 quast --symlink --wt 2

.github/workflows/seacr_callpeak.yml

@@ -0,0 +1,40 @@
+name: seacr_callpeak
+on:
+  push:
+    paths:
+      - software/seacr/callpeak/**
+      - .github/workflows/seacr_callpeak.yml
+      - tests/software/seacr/**
+  pull_request:
+    paths:
+      - software/seacr/callpeak/**
+      - .github/workflows/seacr_callpeak.yml
+      - tests/software/seacr/**
+
+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 seacr_callpeak --symlink --wt 2

.gitignore

@@ -2,5 +2,6 @@
 work/
 results/
 test_output/
+output/
 .DS_Store
 *.code-workspace

.gitmodules

@@ -1,3 +0,0 @@
-[submodule "test-datasets"]
-    path = test-datasets
-    url = https://github.com/nf-core/test-datasets.git

software/bowtie/build/main.nf

@@ -4,7 +4,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
 params.options = [:]
 def options    = initOptions(params.options)
 
-process BOWTIE_INDEX {
+process BOWTIE_BUILD {
     tag "$fasta"
     label 'process_high'
     publishDir "${params.outdir}",
@@ -22,7 +22,7 @@ process BOWTIE_INDEX {
     path fasta
 
     output:
-    path 'bowtie', emit: index
+    path 'bowtie'       , emit: index
     path '*.version.txt', emit: version
 
     script:

software/bowtie/build/meta.yml

@@ -1,4 +1,4 @@
-name: bowtie_index
+name: bowtie_build
 description: Create bowtie index for reference genome
 keywords:
     - index
@@ -49,3 +49,4 @@ output:
           pattern: "*.{version.txt}"
 authors:
     - "@kevinmenden"
+    - "@drpatelh"

software/bowtie2/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/bowtie2/align/main.nf

@@ -0,0 +1,72 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process BOWTIE2_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::bowtie2=2.4.2 bioconda::samtools=1.11 conda-forge::pigz=2.3.4' : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:577a697be67b5ae9b16f637fd723b8263a3898b3-0"
+    } else {
+        container "quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:577a697be67b5ae9b16f637fd723b8263a3898b3-0"
+    }
+
+    input:
+    tuple val(meta), path(reads)
+    path  index
+
+    output:
+    tuple val(meta), path('*.bam'), emit: bam
+    tuple val(meta), path('*.log'), 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}"
+    if (meta.single_end) {
+        def unaligned = params.save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
+        """
+        INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
+        bowtie2 \\
+            -x \$INDEX \\
+            -U $reads \\
+            --threads $task.cpus \\
+            $unaligned \\
+            $options.args \\
+            2> ${prefix}.bowtie2.log \\
+            | samtools view -@ $task.cpus $options.args2 -bhS -o ${prefix}.bam -
+
+        echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//' > ${software}.version.txt
+        """
+    } else {
+        def unaligned = params.save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
+        """
+        INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
+        bowtie2 \\
+            -x \$INDEX \\
+            -1 ${reads[0]} \\
+            -2 ${reads[1]} \\
+            --threads $task.cpus \\
+            $unaligned \\
+            $options.args \\
+            2> ${prefix}.bowtie2.log \\
+            | samtools view -@ $task.cpus $options.args2 -bhS -o ${prefix}.bam -
+
+        if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
+            mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
+        fi
+        if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
+            mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
+        fi
+        echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//' > ${software}.version.txt
+        """
+    }
+}

software/bowtie2/align/meta.yml

@@ -0,0 +1,74 @@
+name: bowtie2_align
+description: Align reads to a reference genome using bowtie2
+keywords:
+    - align
+    - fasta
+    - genome
+    - reference
+tools:
+    - bowtie2:
+          description: |
+              Bowtie 2 is an ultrafast and memory-efficient tool for aligning
+              sequencing reads to long reference sequences.
+          homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
+          documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
+          doi: 10.1038/nmeth.1923
+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: Bowtie2 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"
+    - log:
+        type: file
+        description: Aligment log
+        pattern: "*.log"
+authors:
+    - "@joseespinosa"
+    - "@drpatelh"

software/bowtie2/build/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/bowtie2/build/main.nf

@@ -0,0 +1,35 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process BOWTIE2_BUILD {
+    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::bowtie2=2.4.2' : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.2--py38h1c8e9b9_1'
+    } else {
+        container 'quay.io/biocontainers/bowtie2:2.4.2--py38h1c8e9b9_1'
+    }
+
+    input:
+    path fasta
+
+    output:
+    path 'bowtie2'      , emit: index
+    path '*.version.txt', emit: version
+
+    script:
+    def software  = getSoftwareName(task.process)
+    """
+    mkdir bowtie2
+    bowtie2-build $options.args --threads $task.cpus $fasta bowtie2/${fasta.baseName}
+    echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//' > ${software}.version.txt
+    """
+}

software/bowtie2/build/meta.yml

@@ -0,0 +1,53 @@
+name: bowtie2_build
+description: Builds bowtie index for reference genome
+keywords:
+    - build
+    - index
+    - fasta
+    - genome
+    - reference
+tools:
+    - bowtie2:
+          description: |
+              Bowtie 2 is an ultrafast and memory-efficient tool for aligning
+              sequencing reads to long reference sequences.
+          homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
+          documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
+          doi: 10.1038/nmeth.1923
+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: Bowtie2 genome index files
+          pattern: "*.bt2"
+    - version:
+          type: file
+          description: File containing software version
+          pattern: "*.{version.txt}"
+authors:
+    - "@joseespinosa"
+    - "@drpatelh"

software/fastp/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  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/fastp/main.nf

@@ -0,0 +1,72 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process FASTP {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    conda (params.enable_conda ? 'bioconda::fastp=0.20.1' : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container 'https://depot.galaxyproject.org/singularity/fastp:0.20.1--h8b12597_0'
+    } else {
+        container 'quay.io/biocontainers/fastp:0.20.1--h8b12597_0'
+    }
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path('*.trim.fastq.gz'), emit: reads
+    tuple val(meta), path('*.json')         , emit: json
+    tuple val(meta), path('*.html')         , emit: html
+    tuple val(meta), path('*.log')          , emit: log
+    path '*.version.txt'                    , emit: version
+    tuple val(meta), path('*.fail.fastq.gz'), optional:true, emit: reads_fail
+
+    script:
+    // Added soft-links to original fastqs for consistent naming in MultiQC
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    if (meta.single_end) {
+        def fail_fastq = params.save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : ''
+        """
+        [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
+        fastp \\
+            --in1 ${prefix}.fastq.gz \\
+            --out1 ${prefix}.trim.fastq.gz \\
+            --thread $task.cpus \\
+            --json ${prefix}.fastp.json \\
+            --html ${prefix}.fastp.html \\
+            $fail_fastq \\
+            $options.args \\
+            2> ${prefix}.fastp.log
+        echo \$(fastp --version 2>&1) | sed -e "s/fastp //g" > ${software}.version.txt
+        """
+    } else {
+        def fail_fastq = params.save_trimmed_fail ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : ''
+        """
+        [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
+        [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
+        fastp \\
+            --in1 ${prefix}_1.fastq.gz \\
+            --in2 ${prefix}_2.fastq.gz \\
+            --out1 ${prefix}_1.trim.fastq.gz \\
+            --out2 ${prefix}_2.trim.fastq.gz \\
+            --json ${prefix}.fastp.json \\
+            --html ${prefix}.fastp.html \\
+            $fail_fastq \\
+            --thread $task.cpus \\
+            --detect_adapter_for_pe \\
+            $options.args \\
+            2> ${prefix}.fastp.log
+
+        echo \$(fastp --version 2>&1) | sed -e "s/fastp //g" > ${software}.version.txt
+        """
+    }
+}

software/fastp/meta.yml

@@ -0,0 +1,79 @@
+name: fastp
+description: Perform adapter/quality trimming on sequencing reads
+keywords:
+  - trimming
+  - quality control
+  - fastq
+tools:
+  - fastq:
+      description: |
+        A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
+      documentation: https://github.com/OpenGene/fastp
+      doi: https://doi.org/10.1093/bioinformatics/bty560
+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:
+  - 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.
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: The trimmed/modified fastq reads
+      pattern: "*trim.fastq.gz"
+  - json:
+      type: file
+      description: Results in JSON format
+      pattern: "*.json"
+  - html:
+      type: file
+      description: Results in HTML format
+      pattern: "*.thml"
+  - log:
+      type: file
+      description: fastq log file
+      pattern: "*.log"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - reads_fail:
+      type: file
+      description: Reads the failed the preprocessing
+      pattern: "*fail.fastq.gz"
+authors:
+  - "@drpatelh"
+  - "@kevinmenden"

software/quast/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  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/quast/main.nf

@@ -0,0 +1,48 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process QUAST {
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+
+    conda (params.enable_conda ? 'bioconda::quast=5.0.2' : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container 'https://depot.galaxyproject.org/singularity/quast:5.0.2--py37pl526hb5aa323_2'
+    } else {
+        container 'quay.io/biocontainers/quast:5.0.2--py37pl526hb5aa323_2'
+    }
+
+    input:
+    path consensus
+    path fasta
+    path gff
+    val use_fasta
+    val use_gff
+
+    output:
+    path "${prefix}"    , emit: results
+    path '*.tsv'        , emit: tsv
+    path '*.version.txt', emit: version
+
+    script:
+    def software  = getSoftwareName(task.process)
+    prefix        = options.suffix ?: software
+    def features  = use_gff ? "--features $gff" : ''
+    def reference = use_fasta ? "-r $fasta" : ''
+    """
+    quast.py \\
+        --output-dir $prefix \\
+        $reference \\
+        $features \\
+        --threads $task.cpus \\
+        $options.args \\
+        ${consensus.join(' ')}
+    ln -s ${prefix}/report.tsv
+    echo \$(quast.py --version 2>&1) | sed 's/^.*QUAST v//; s/ .*\$//' > ${software}.version.txt
+    """
+}

software/quast/meta.yml

@@ -0,0 +1,68 @@
+name: quast
+description: Quality Assessment Tool for Genome Assemblies
+keywords:
+  - quast
+  - assembly
+  - quality
+tools:
+  - quast:
+      description: |
+        QUAST calculates quality metrics for genome assemblies
+      homepage: http://bioinf.spbau.ru/quast
+      doi:
+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:
+  - consensus:
+      type: file
+      description: |
+        Fasta file containing the assembly of interest
+  - fasta:
+      type: file
+      description: |
+        The genome assembly to be evaluated. Has to contain at least a non-empty string dummy value.
+  - use_fasta:
+      type: boolean
+      description: Whether to use the provided fasta reference genome file
+  - gff:
+      type: file
+      description: The genome GFF file. Has to contain at least a non-empty string dummy value.
+  - use_gff:
+      type: boolean
+      description: Whether to use the provided gff reference annotation file
+
+output:
+  - quast:
+      type: directory
+      description: Directory containing complete quast report
+      pattern: "{prefix}.lineage_report.csv"
+  - report:
+
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+
+authors:
+  - "@drpatelh"
+  - "@kevinmenden"

software/seacr/callpeak/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  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/seacr/callpeak/main.nf

@@ -0,0 +1,42 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+def VERSION = '1.3'
+
+process SEACR_CALLPEAK {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.29.2" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:5bb5ed4307a8187a7f34730b00431de93688fa59-0"
+    } else {
+        container 'quay.io/biocontainers/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:5bb5ed4307a8187a7f34730b00431de93688fa59-0'
+    }
+
+    input:
+    tuple val(meta), path(bedgraph), path(ctrlbedgraph)
+
+    output:
+    tuple val(meta), path("*.bed"), emit: bed
+    path "*.version.txt"          , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    SEACR_1.3.sh \\
+        $bedgraph \\
+        $ctrlbedgraph \\
+        $options.args \\
+        $prefix
+
+    echo $VERSION > ${software}.version.txt
+    """
+}

software/seacr/callpeak/meta.yml

@@ -0,0 +1,69 @@
+name: seacr_callpeak
+description: Call peaks using SEACR on sequenced reads in bedgraph format
+keywords:
+    - peak-caller
+    - peaks
+    - bedgraph
+    - cut&tag
+    - cut&run
+    - chromatin
+    - seacr
+tools:
+    - seacr:
+        description: |
+            SEACR is intended to call peaks and enriched regions from sparse CUT&RUN
+            or chromatin profiling data in which background is dominated by "zeroes"
+            (i.e. regions with no read coverage).
+        homepage: https://github.com/FredHutch/SEACR
+        documentation: https://github.com/FredHutch/SEACR
+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:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bedgraph:
+        type: file
+        description: |
+            The target bedgraph file from which the peaks will be calculated.
+    - ctrlbedgraph:
+        type: file
+        description: |
+            Control (IgG) data bedgraph file to generate an empirical threshold for peak calling.
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bed:
+        type: file
+        description: Bed file containing the calculated peaks.
+        pattern: "*.bed"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@chris-cheshire"

tests/software/bowtie/main.nf

@@ -2,32 +2,32 @@
 
 nextflow.enable.dsl = 2
 
-include { BOWTIE_INDEX } from '../../../software/bowtie/index/main.nf' addParams( options: [:] )
+include { BOWTIE_BUILD } from '../../../software/bowtie/build/main.nf' addParams( options: [:] )
 include { BOWTIE_ALIGN } from '../../../software/bowtie/align/main.nf'  addParams( options: [:] )
 
-workflow test_bowtie_index {
+workflow test_bowtie_build {
     fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
-    BOWTIE_INDEX ( fasta ) 
+    BOWTIE_BUILD ( fasta )
 }
 
 workflow test_bowtie_alignment_single_end {
 
     fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
-    BOWTIE_INDEX ( fasta ) 
+    BOWTIE_BUILD ( 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 )
+    BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
 }
 
 workflow test_bowtie_alignment_paired_end {
     fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
-    BOWTIE_INDEX ( fasta ) 
+    BOWTIE_BUILD ( 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 )
+    BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
 }

tests/software/bowtie/test.yml

@@ -1,8 +1,8 @@
-- name: Run bowtie index
-  command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_index -c tests/config/nextflow.config
+- name: Run bowtie build
+  command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_build -c tests/config/nextflow.config
   tags:
     - bowtie
-    - bowtie_index
+    - bowtie_build
   files:
     - path: output/bowtie/bowtie/NC_010473.1.ebwt
       md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
@@ -17,7 +17,7 @@
     - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
       md5sum: f3c398bba5158f4039334a932d79c051
 
-- name: Run bowtie index and align single-end
+- name: Run bowtie build 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

tests/software/bowtie2/main.nf

@@ -0,0 +1,33 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BOWTIE2_BUILD } from '../../../software/bowtie2/build/main.nf' addParams( options: [:] )
+include { BOWTIE2_ALIGN } from '../../../software/bowtie2/align/main.nf'  addParams( options: [:] )
+
+workflow test_bowtie2_build {
+    fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    BOWTIE2_BUILD ( fasta )
+}
+
+workflow test_bowtie2_alignment_single_end {
+
+    fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    BOWTIE2_BUILD ( fasta )
+
+    def input = []
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ]
+    BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index )
+}
+
+workflow test_bowtie2_alignment_paired_end {
+    fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    BOWTIE2_BUILD ( 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) ] ]
+    BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index )
+}

tests/software/bowtie2/test.yml

@@ -0,0 +1,64 @@
+- name: Run bowtie2 build
+  command: nextflow run ./tests/software/bowtie2 -profile docker -entry test_bowtie2_build -c tests/config/nextflow.config
+  tags:
+    - bowtie2
+    - bowtie2_build
+  files:
+    - path: output/bowtie2/bowtie2/NC_010473.1.bt2
+      md5sum: 4db22d92e72111a5fbf609b3d9a43015
+    - path: output/bowtie2/bowtie2/NC_010473.2.bt2
+      md5sum: f4429ec74ee0064732c4bb26718a3eb1
+    - path: output/bowtie2/bowtie2/NC_010473.3.bt2
+      md5sum: cd201e81724f3099131aec16ef2cc53b
+    - path: output/bowtie2/bowtie2/NC_010473.4.bt2
+      md5sum: bbb9d6d21ad765d135f95290204e8433
+    - path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2
+      md5sum: 4ccfee8857c3b1c69857e5ecdef597aa
+    - path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2
+      md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72
+
+- name: Run bowtie2 index and align single-end
+  command: nextflow run ./tests/software/bowtie2 -profile docker -entry test_bowtie2_alignment_single_end -c tests/config/nextflow.config
+  tags:
+    - bowtie2
+    - bowtie2_align
+  files:
+    - path: output/bowtie2/bowtie2/NC_010473.1.bt2
+      md5sum: 4db22d92e72111a5fbf609b3d9a43015
+    - path: output/bowtie2/bowtie2/NC_010473.2.bt2
+      md5sum: f4429ec74ee0064732c4bb26718a3eb1
+    - path: output/bowtie2/bowtie2/NC_010473.3.bt2
+      md5sum: cd201e81724f3099131aec16ef2cc53b
+    - path: output/bowtie2/bowtie2/NC_010473.4.bt2
+      md5sum: bbb9d6d21ad765d135f95290204e8433
+    - path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2
+      md5sum: 4ccfee8857c3b1c69857e5ecdef597aa
+    - path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2
+      md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72
+    - path: output/bowtie2/test.bowtie2.log
+      md5sum: 90041c264231be535042adb93a279356
+    - path: output/bowtie2/test.bam
+      md5sum: 906102f401d8234b6473790988fb09cf
+
+- name: Run bowtie2 index and align paired-end
+  command: nextflow run ./tests/software/bowtie2 -profile docker -entry test_bowtie2_alignment_paired_end -c tests/config/nextflow.config
+  tags:
+    - bowtie2
+    - bowtie2_align
+  files:
+    - path: output/bowtie2/bowtie2/NC_010473.1.bt2
+      md5sum: 4db22d92e72111a5fbf609b3d9a43015
+    - path: output/bowtie2/bowtie2/NC_010473.2.bt2
+      md5sum: f4429ec74ee0064732c4bb26718a3eb1
+    - path: output/bowtie2/bowtie2/NC_010473.3.bt2
+      md5sum: cd201e81724f3099131aec16ef2cc53b
+    - path: output/bowtie2/bowtie2/NC_010473.4.bt2
+      md5sum: bbb9d6d21ad765d135f95290204e8433
+    - path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2
+      md5sum: 4ccfee8857c3b1c69857e5ecdef597aa
+    - path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2
+      md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72
+    - path: output/bowtie2/test.bowtie2.log
+      md5sum: 9f9eb40b5f57e0f2d5c874f2c1b5cfd5
+    - path: output/bowtie2/test.bam
+      md5sum: 732a33cd9816b38ea9b919c25eeb78f8

tests/software/fastp/main.nf

@@ -0,0 +1,30 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FASTP } from '../../../software/fastp/main.nf'  addParams( options: [:] )
+
+/*
+ * Test with single-end data
+ */
+workflow test_fastp_se {
+    def input = []
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
+
+    FASTP( input )
+}
+
+/*
+ * Test with paired-end data
+ */
+
+workflow test_fastp_pe {
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
+                file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
+
+    FASTP( input )
+}
+

tests/software/fastp/test.yml

@@ -0,0 +1,27 @@
+- name: fastp_se
+  command: nextflow run ./tests/software/fastp -profile docker -entry test_fastp_se -c ./tests/config/nextflow.config
+  tags:
+    - fastp
+    - fastp_se
+  files:
+    - path: ./output/fastp/test.fastp.json
+      md5sum: b81d53bfa5c1553bed89f6475edcf437
+    - path: ./output/fastp/test.trim.fastq.gz
+      md5sum: 2f5516df477b123e3f78adb67effa3bc
+    - path: ./output/fastp/test.fastp.log
+    - path: ./output/fastp/test.fastp.html
+
+- name: fastp_pe
+  command: nextflow run ./tests/software/fastp -profile docker -entry test_fastp_pe -c ./tests/config/nextflow.config
+  tags:
+    - fastp
+    - fastp_pe
+  files:
+    - path: ./output/fastp/test.fastp.html
+    - path: ./output/fastp/test.fastp.json
+      md5sum: 40db7fcbed478b0a96a1c5c1bb5f737b
+    - path: ./output/fastp/test.fastp.log
+    - path: ./output/fastp/test_1.trim.fastq.gz
+      md5sum: c8844c05194b50ae368e6825e997aa7f
+    - path: ./output/fastp/test_2.trim.fastq.gz
+      md5sum: 9238b07bb1609e939be7c8889b72c209

tests/software/quast/main.nf

@@ -0,0 +1,25 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { QUAST }   from '../../../software/quast/main.nf'   addParams(options: [:])
+
+workflow test_quast_ref {
+    consensus = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
+    gff = file("${launchDir}/tests/data/gff/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true)
+    fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
+    def use_fasta = true
+    def use_gtf = true
+
+    QUAST( consensus, fasta, gff, use_fasta, use_gtf )
+}
+
+workflow test_quast_noref {
+    consensus = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
+    gff = file('gff_dummy')
+    fasta = file('fasta_dummy')
+    def use_fasta = false
+    def use_gtf = false
+
+    QUAST( consensus, fasta, gff, use_fasta, use_gtf )
+}

tests/software/quast/test.yml

@@ -0,0 +1,120 @@
+- name: quast_ref
+  command: nextflow run ./tests/software/quast -profile docker -entry test_quast_ref -c ./tests/config/nextflow.config
+  tags:
+    - quast
+    - quast_reference
+  files:
+    - path: ./output/quast/quast/basic_stats/NGx_plot.pdf
+    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords.filtered
+      md5sum: ec9191d0acb5d5bce56b4842551a8598
+    - path: ./output/quast/quast/aligned_stats/NGAx_plot.pdf
+    - path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html
+      md5sum: c42838b1553759fb0460a9854e39da36
+    - path: ./output/quast/report.tsv
+      md5sum: b203a9d2c995bd66552eeb5cb0a98762
+    - path: ./output/quast/quast/report.tex
+      md5sum: 8168f197dfb2f781accdefaa0d90fc87
+    - path: ./output/quast/quast/contigs_reports/misassemblies_frcurve_plot.pdf
+    - path: ./output/quast/quast/transposed_report.tex
+      md5sum: 0b8fd00649a5758024c8093d5919f71c
+    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords
+      md5sum: dda3fc0addc41ecc0d5183dee6f95886
+    - path: ./output/quast/quast/transposed_report.txt
+      md5sum: 73216314e65ef91c24422d5bdd0795e4
+    - path: ./output/quast/quast/report.html
+    - path: ./output/quast/quast/report.pdf
+    - path: ./output/quast/quast/contigs_reports/all_alignments_GCA_011545545-1_ASM1154554v1_cds_from_genomic.tsv
+      md5sum: c247152eb82b361106492642fd796e2c
+    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.used_snps.gz
+      md5sum: 7b1db1b433cd95243a949bcb72e7e3a6
+    - path: ./output/quast/quast/contigs_reports/unaligned_report.tex
+      md5sum: 48562e30903fcf33946e13b602b0e324
+    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.sf
+    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.txt
+      md5sum: 53c481fe8b3ef18280ea86cbded78b31
+    - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.mis_contigs.info
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: ./output/quast/quast/contigs_reports/unaligned_report.tsv
+      md5sum: 769f2d9d7deb5e7a63e238d8ba0cfe13
+    - path: ./output/quast/quast/basic_stats/GCA_011545545.1_ASM1154554v1_cds_from_genomic_GC_content_plot.pdf
+    - path: ./output/quast/quast/genome_stats/features_cumulative_plot.pdf
+    - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf
+    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tex
+      md5sum: 85614257e0bb62ac750f7872886b2fbf
+    - path: ./output/quast/quast/quast.log
+    - path: ./output/quast/quast/contigs_reports/misassemblies_report.tsv
+      md5sum: 33144f8d064782864e8400e3a08b2a3a
+    - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.unaligned.info
+      md5sum: a8505cf206bf53ca369f7e3073fee587
+    - path: ./output/quast/quast/genome_stats/GCA_011545545-1_ASM1154554v1_cds_from_genomic_genomic_features_any.txt
+      md5sum: 307b3bb1f42fc2f11a60a2e9846021d7
+    - path: ./output/quast/quast/icarus.html
+      md5sum: 6e57f5f7d07528496fc2f35b449951fe
+    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tsv
+      md5sum: 4d24cc0da823a100a076aef36f9fd75e
+    - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.stderr
+    - path: ./output/quast/quast/aligned_stats/cumulative_plot.pdf
+    - path: ./output/quast/quast/genome_stats/genome_info.txt
+      md5sum: bc3df27ad7356c045c9a108f9d4bcfbe
+    - path: ./output/quast/quast/genome_stats/features_frcurve_plot.pdf
+    - path: ./output/quast/quast/contigs_reports/misassemblies_report.txt
+      md5sum: 0784e0d31e9f2a165730cc0029023427
+    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.unaligned
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.stdout
+    - path: ./output/quast/quast/contigs_reports/unaligned_report.txt
+      md5sum: c1c26797084ea743ec5a224ab97adb1f
+    - path: ./output/quast/quast/genome_stats/GCA_011545545-1_ASM1154554v1_cds_from_genomic_gaps.txt
+      md5sum: c52381f09ea40b6141be5232494727b6
+    - path: ./output/quast/quast/icarus_viewers/alignment_viewer.html
+      md5sum: ad5176f21d3c4809a9a8f9c27bb8d70a
+    - path: ./output/quast/quast/contigs_reports/misassemblies_report.tex
+      md5sum: ffe19cf4d5332952f0627e9cd82e3375
+    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords_tmp
+      md5sum: ce66eaeb99fdc11e4d50efadc1816e04
+    - path: ./output/quast/quast/basic_stats/gc.icarus.txt
+      md5sum: b3a770802ff9b2dd4ee8e47bddb2df3e
+    - path: ./output/quast/quast/basic_stats/Nx_plot.pdf
+    - path: ./output/quast/quast/transposed_report.tsv
+      md5sum: 1754bd6c6fa8a0172a342a48dd3ca505
+    - path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
+    - path: ./output/quast/quast/report.txt
+      md5sum: e334b3390a5028cbf88fe4ccab2b6499
+    - path: ./output/quast/quast/contigs_reports/misassemblies_plot.pdf
+    - path: ./output/quast/quast/report.tsv
+      md5sum: b203a9d2c995bd66552eeb5cb0a98762
+    - path: ./output/quast/quast/contigs_reports/GCA_011545545_1_ASM1154554v1_cds_from_genomic.mis_contigs.fa
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: ./output/quast/quast/aligned_stats/NAx_plot.pdf
+
+- name: quast_noref
+  command: nextflow run ./tests/software/quast -profile docker -entry test_quast_noref -c ./tests/config/nextflow.config
+  tags:
+    - quast
+    - quast_no_reference
+  files:
+    - path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html
+      md5sum: d2680b8083139e62baf7af0f852d52b8
+    - path: ./output/quast/quast/transposed_report.txt
+      md5sum: b6b126e9dcfd8c8e7bd36dff9220caf0
+    - path: ./output/quast/report.tsv
+      md5sum: 55d2938fcdb678e97d441cf32b9c740e
+    - path: ./output/quast/quast/icarus.html
+      md5sum: dcb11b4c7b6c21190c1344c46288d3f4
+    - path: ./output/quast/quast/report.txt
+      md5sum: c8e87f40e888a0395be04f78532d9deb
+    - path: ./output/quast/quast/transposed_report.tsv
+      md5sum: 27b6c755be5d70e3eed22e1bf3f68ce5
+    - path: ./output/quast/quast/quast.log
+    - path: ./output/quast/quast/report.tex
+      md5sum: 69c31172ae6257663b22bb192ba84682
+    - path: ./output/quast/quast/report.pdf
+    - path: ./output/quast/quast/basic_stats/GCA_011545545.1_ASM1154554v1_cds_from_genomic_GC_content_plot.pdf
+    - path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
+    - path: ./output/quast/quast/report.tsv
+      md5sum: 55d2938fcdb678e97d441cf32b9c740e
+    - path: ./output/quast/quast/transposed_report.tex
+      md5sum: 213fb615afe21904e52d670e602c1f62
+    - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf
+    - path: ./output/quast/quast/basic_stats/Nx_plot.pdf
+    - path: ./output/quast/quast/report.html

tests/software/seacr/main.nf

@@ -0,0 +1,20 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEACR_CALLPEAK } from '../../../software/seacr/callpeak/main.nf' addParams( options: [ args:'norm stringent' ] )
+
+workflow test_seacr_callpeak {
+
+    def input = []
+    input = [[ id:'test_1'],
+              file("${launchDir}/tests/data/bedgraph/K27me3_1_to_chr20.bedgraph", checkIfExists: true),
+              file("${launchDir}/tests/data/bedgraph/IgG_1_to_chr20.bedgraph", checkIfExists: true) ]
+
+    SEACR_CALLPEAK ( input )
+}
+
+// For local testing
+workflow {
+    test_seacr_callpeak()
+}

tests/software/seacr/test.yml

@@ -0,0 +1,8 @@
+- name: Run seacr call peak test workflow
+  command: nextflow run ./tests/software/seacr/ -profile docker -entry test_seacr_callpeak -c tests/config/nextflow.config
+  tags:
+    - seacr
+    - seacr_callpeak
+  files:
+    - path: output/seacr/test_1.stringent.bed
+      md5sum: 3ac70475669eb6a7b8ca89e19a08a28e