module: bwa/sampe (#625)

* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Add bwa/aln module

* Also output reads as required with SAI

* Add sampe

* Fix container paths

* Update based on code review from @grst

* Update input docs

modules/bwa/sampe/functions.nf

@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${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/bwa/sampe/main.nf

@@ -0,0 +1,46 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process BWA_SAMPE {
+    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), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0"
+    } else {
+        container "quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0"
+    }
+
+    input:
+    tuple val(meta), path(reads), path(sai)
+    path index
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    path "*.version.txt"          , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def read_group = meta.read_group ? "-r ${meta.read_group}" : ""
+
+    """
+    INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
+
+    bwa sampe \\
+        $options.args \\
+        $read_group \\
+        \$INDEX \\
+        $sai \\
+        $reads | samtools sort -@ ${task.cpus - 1} -O bam - > ${prefix}.bam
+
+    echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
+    """
+}

modules/bwa/sampe/meta.yml

@@ -0,0 +1,58 @@
+name: bwa_sampe
+description: Convert paired-end bwa SA coordinate files to SAM format
+keywords:
+  - bwa
+  - aln
+  - short-read
+  - align
+  - reference
+  - fasta
+  - map
+  - sam
+  - bam
+tools:
+    - bwa:
+        description: |
+            BWA is a software package for mapping DNA sequences against
+            a large reference genome, such as the human genome.
+        homepage: http://bio-bwa.sourceforge.net/
+        documentation: http://bio-bwa.sourceforge.net/
+        doi: "10.1093/bioinformatics/btp324"
+      licence: ['GPL v3']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information.
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: FASTQ files specified alongside meta in input channel.
+      pattern: "*.{fastq,fq}.gz"
+  - sai:
+      type: file
+      description: SAI file specified alongside meta and reads in input channel.
+      pattern: "*.sai"
+  - index:
+        type: directory
+        description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX
+        pattern: "bwa/"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - bam:
+      type: file
+      description: BAM file
+      pattern: "*.bam"
+
+authors:
+  - "@jfy133"

tests/config/pytest_modules.yml

@@ -170,6 +170,10 @@ bwa/mem:
   - modules/bwa/mem/**
   - tests/modules/bwa/mem/**
 
+bwa/sampe:
+  - modules/bwa/sampe/**
+  - tests/modules/bwa/sampe/**
+
 bwa/samse:
   - modules/bwa/samse/**
   - tests/modules/bwa/samse/**

tests/modules/bwa/sampe/main.nf

@@ -0,0 +1,20 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' addParams( options: [:] )
+include { BWA_ALN } from '../../../../modules/bwa/aln/main.nf' addParams( options: [:] )
+include { BWA_SAMPE } from '../../../../modules/bwa/sampe/main.nf' addParams( options: [:] )
+
+workflow test_bwa_sampe {
+
+    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) ]
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BWA_INDEX ( fasta )
+    BWA_ALN ( input, BWA_INDEX.out.index )
+    BWA_SAMPE ( BWA_ALN.out.sai, BWA_INDEX.out.index )
+}

tests/modules/bwa/sampe/test.yml

@@ -0,0 +1,8 @@
+- name: bwa sampe
+  command: nextflow run ./tests/modules/bwa/sampe -entry test_bwa_sampe -c tests/config/nextflow.config
+  tags:
+    - bwa
+    - bwa/sampe
+  files:
+    - path: output/bwa/test.bam
+      md5sum: f6ad85d66d44c5d26e692109d2e34100