Merge pull request #110 from luslab/master

Add SEACR module containing a single CALLPEAK process

.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/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/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