new module: AdapterRemoval (#309)

* add adapterremoval module

* fix indentations

* switch to process_medium

* update docker tests

* remove duplicated entry

* fix line ending

* Update software/adapterremoval/main.nf

* Update software/adapterremoval/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

software/adapterremoval/functions.nf

@@ -0,0 +1,60 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.args3         = args.args3 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/adapterremoval/main.nf

@@ -0,0 +1,80 @@
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process ADAPTERREMOVAL {
+    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::adapterremoval=2.3.2" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/adapterremoval:2.3.2--hb7ba0dd_0"
+    } else {
+        container "quay.io/biocontainers/adapterremoval:2.3.2--hb7ba0dd_0"
+    }
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path('*.fastq.gz'), emit: reads
+    tuple val(meta), path('*.log')     , emit: log
+    path "*.version.txt"               , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+
+    if (meta.single_end) {
+        """
+        AdapterRemoval  \\
+            --file1 $reads \\
+            $options.args \\
+            --basename $prefix \\
+            --threads $task.cpus \\
+            --settings ${prefix}.log \\
+            --output1 ${prefix}.trimmed.fastq.gz \\
+            --seed 42 \\
+            --gzip \\
+
+        AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g" > ${software}.version.txt
+        """
+    } else if (!meta.single_end && !meta.collapse) {
+        """
+        AdapterRemoval  \\
+            --file1 ${reads[0]} \\
+            --file2 ${reads[0]} \\
+            $options.args \\
+            --basename $prefix \\
+            --threads $task.cpus \\
+            --settings ${prefix}.log \\
+            --output1 ${prefix}.pair1.trimmed.fastq.gz \\
+            --output2 ${prefix}.pair2.trimmed.fastq.gz \\
+            --seed 42 \\
+            --gzip \\
+
+        AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g" > ${software}.version.txt
+        """
+    } else {
+        """
+        AdapterRemoval  \\
+            --file1 ${reads[0]} \\
+            --file2 ${reads[0]} \\
+            --collapse \\
+            $options.args \\
+            --basename $prefix \\
+            --threads $task.cpus \\
+            --settings ${prefix}.log \\
+            --seed 42 \\
+            --gzip \\
+
+        cat *.collapsed.gz *.collapsed.truncated.gz > ${prefix}.merged.fastq.gz
+        AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g" > ${software}.version.txt
+        """
+    }
+
+}

software/adapterremoval/meta.yml

@@ -0,0 +1,50 @@
+name: adapterremoval
+description: Trim sequencing adapters and collapse overlapping reads
+keywords:
+    - trimming
+    - adapters
+    - merging
+    - fastq
+tools:
+    - adapterremoval:
+        description: The AdapterRemoval v2 tool for merging and clipping reads.
+        homepage: https://github.com/MikkelSchubert/adapterremoval
+        documentation: https://adapterremoval.readthedocs.io
+        licence: ['GPL v3']
+
+input:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false, collapse:false ]
+    - reads:
+        type: file
+        description: |
+          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+          respectively.
+        pattern: "*.{fq,fastq,fg.gz,fastq.gz}"
+
+output:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: |
+          List of input adapter trimmed FastQ files of size 1 or 2 for
+          single-end or collapsed data and paired-end data, respectively.
+        pattern: "*.{fastq.gz}"
+    - log:
+        type: file
+        description: AdapterRemoval log file
+        pattern: "*.log"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+
+authors:
+    - "@maxibor"

tests/config/pytest_software.yml

@@ -1,3 +1,7 @@
+adapterremoval:
+  - software/adapterremoval/**
+  - tests/software/adapterremoval/**
+
 bandage_image:
   - software/bandage/image/**
   - tests/software/bandage/image/**
@@ -76,11 +80,6 @@ bismark_methylationextractor:
   - software/bismark/genomepreparation/**
   - tests/software/bismark/methylationextractor/**
 
-
-blast_blastn:
-  - software/blast/blastn/**
-  - tests/software/blast/blastn/**
-
 bismark_report:
   - software/bismark/genomepreparation/**
   - software/bismark/align/**
@@ -97,6 +96,10 @@ bismark_summary:
   - software/bismark/summary/**
   - tests/software/bismark/summary/**
 
+blast_blastn:
+  - software/blast/blastn/**
+  - tests/software/blast/blastn/**
+
 blast_makeblastdb:
   - software/blast/makeblastdb/**
   - tests/software/blast/makeblastdb/**

tests/software/adapterremoval/main.nf

@@ -0,0 +1,35 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ADAPTERREMOVAL } from '../../../software/adapterremoval/main.nf' addParams( options: [:] )
+
+workflow test_adapterremoval_single_end {
+    
+    def input = []
+    input = [ [ id:'test', single_end:true, collapse:false ], // meta map
+              file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ]
+
+    ADAPTERREMOVAL ( input )
+}
+
+workflow test_adapterremoval_paired_end {
+    
+    def input = []
+    input = [ [ id:'test', single_end:false, collapse:false ], // meta map
+              [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true),
+                file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true) ]]
+
+    ADAPTERREMOVAL ( input )
+}
+
+workflow test_adapterremoval_paired_end_collapse {
+    
+    def input = []
+    input = [ [ id:'test', single_end:false, collapse:true ], // meta map
+              [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true),
+                file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true) ]]
+
+    ADAPTERREMOVAL ( input )
+}
+

tests/software/adapterremoval/test.yml

@@ -0,0 +1,34 @@
+- name: adapterremoval test_adapterremoval_single_end
+  command: nextflow run tests/software/adapterremoval -entry test_adapterremoval_single_end -c tests/config/nextflow.config
+  tags:
+    - adapterremoval_single_end
+    - adapterremoval
+  files:
+    - path: output/adapterremoval/test.log
+      md5sum: 2fd3d5d703b63ba33a83021fccf25f77
+    - path: output/adapterremoval/test.trimmed.fastq.gz
+      md5sum: 62139afee94defad5b83bdd0b8475a1f
+
+- name: adapterremoval test_adapterremoval_paired_end
+  command: nextflow run tests/software/adapterremoval -entry test_adapterremoval_paired_end -c tests/config/nextflow.config
+  tags:
+    - adapterremoval_paired_end
+    - adapterremoval
+  files:
+    - path: output/adapterremoval/test.pair2.trimmed.fastq.gz
+      md5sum: f076a9f666235e01a3281f8c46c9d010
+    - path: output/adapterremoval/test.log
+      md5sum: bea86105aff4d27fe29c83e24498fefa
+    - path: output/adapterremoval/test.pair1.trimmed.fastq.gz
+      md5sum: f076a9f666235e01a3281f8c46c9d010
+
+- name: adapterremoval test_adapterremoval_paired_end_collapse
+  command: nextflow run tests/software/adapterremoval -entry test_adapterremoval_paired_end_collapse -c tests/config/nextflow.config
+  tags:
+    - adapterremoval_paired_end_collapse
+    - adapterremoval
+  files:
+    - path: output/adapterremoval/test.log
+      md5sum: 97cb97b3d03123ac88430768b2e36c59
+    - path: output/adapterremoval/test.merged.fastq.gz
+      md5sum: 50a4f9fdac6a24e211eb4dcf9f292bef