New module seqtk/mergepe (#951)

* First step into creating a seqtk/mergepe module to interleave fastQ input

* First rewrite of main.nf to make the module perform the desired (interleave/merge of pe reads) task

* Modifications to test the new seqtk/mergepe module.

* Improving the seqtk/mergepe module to output single end reads as well, and making sure tests work

* Modified so that gzip uses -n and that single read entries are symlinked with ln -s instead of copied, therefore updated test.yml as well.

* Fix trailing whitespaces

Co-authored-by: Daniel Lundin <daniel.lundin@lnu.se>

modules/seqtk/mergepe/functions.nf

@@ -0,0 +1,78 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}

modules/seqtk/mergepe/main.nf

@@ -0,0 +1,53 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process SEQTK_MERGEPE {
+    tag "$meta.id"
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::seqtk=1.3" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3"
+    } else {
+        container "quay.io/biocontainers/seqtk:1.3--h5bf99c6_3"
+    }
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path("*.fastq.gz"), emit: reads
+    path "versions.yml"          , emit: versions
+
+    script:
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    if (meta.single_end) {
+        """
+        ln -s ${reads} ${prefix}.fastq.gz
+
+        cat <<-END_VERSIONS > versions.yml
+        ${getProcessName(task.process)}:
+            ${getSoftwareName(task.process)}: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+        END_VERSIONS
+        """
+    } else {
+        """
+        seqtk \\
+            mergepe \\
+            $options.args \\
+            ${reads} \\
+            | gzip -n >> ${prefix}.fastq.gz
+
+        cat <<-END_VERSIONS > versions.yml
+        ${getProcessName(task.process)}:
+            ${getSoftwareName(task.process)}: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+        END_VERSIONS
+        """
+    }
+}

modules/seqtk/mergepe/meta.yml

@@ -0,0 +1,40 @@
+name: seqtk_mergepe
+description: Interleave pair-end reads from FastQ files
+keywords:
+  - interleave
+tools:
+  - seqtk:
+      description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk mergepe command merges pair-end reads into one interleaved file.
+      homepage: https://github.com/lh3/seqtk
+      documentation:  https://docs.csc.fi/apps/seqtk/
+      tool_dev_url: https://github.com/lh3/seqtk
+      licence: ['MIT']
+
+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.
+      pattern: "*.{fastq.gz}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - reads:
+      type: file
+      description: If single-end reads, the output is the same as the input, 1 FastQ file for each read. If pair-end reads, the read pairs will be interleaved and output as 1 FastQ file for each read pair.
+      pattern: "*.{fastq.gz}"
+
+authors:
+  - "@emnilsson"

tests/config/pytest_modules.yml

@@ -1023,6 +1023,10 @@ seacr/callpeak:
   - modules/seacr/callpeak/**
   - tests/modules/seacr/callpeak/**
 
+seqtk/mergepe:
+  - modules/seqtk/mergepe/**
+  - tests/modules/seqtk/mergepe/**
+
 seqkit/split2:
   - modules/seqkit/split2/**
   - tests/modules/seqkit/split2/**

tests/modules/seqtk/mergepe/main.nf

@@ -0,0 +1,31 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEQTK_MERGEPE } from '../../../../modules/seqtk/mergepe/main.nf' addParams( options: [ 'suffix':'.processed' ] )
+
+//
+// Test with single-end data
+//
+
+workflow test_seqtk_mergepe_single_end {
+
+    input = [ [ id:'test', single_end:true ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+
+    SEQTK_MERGEPE ( input )
+}
+
+//
+// Test with paired-end data
+//
+
+workflow test_seqtk_mergepe_paired_end {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    SEQTK_MERGEPE ( input )
+}

tests/modules/seqtk/mergepe/test.yml

@@ -0,0 +1,17 @@
+- name: seqtk mergepe test_seqtk_mergepe_single_end
+  command: nextflow run tests/modules/seqtk/mergepe -entry test_seqtk_mergepe_single_end -c tests/config/nextflow.config
+  tags:
+    - seqtk/mergepe
+    - seqtk
+  files:
+    - path: output/seqtk/test.processed.fastq.gz
+      md5sum: e325ef7deb4023447a1f074e285761af
+
+- name: seqtk mergepe test_seqtk_mergepe_paired_end
+  command: nextflow run tests/modules/seqtk/mergepe -entry test_seqtk_mergepe_paired_end -c tests/config/nextflow.config
+  tags:
+    - seqtk/mergepe
+    - seqtk
+  files:
+    - path: output/seqtk/test.processed.fastq.gz
+      md5sum: 3f094ef62d9bfe06aa25174a06bc7d04