Bbmap index (#683)

BBMap index module

modules/bbmap/index/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/bbmap/index/main.nf

@@ -0,0 +1,39 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process BBMAP_INDEX {
+    tag "$fasta"
+    label 'process_long'
+    publishDir "${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::bbmap=38.92" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bbmap:38.92--he522d1c_0"
+    } else {
+        container "quay.io/biocontainers/bbmap:38.92--he522d1c_0"
+    }
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path('ref')  , emit: index
+    path "*.version.txt"          , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    """
+    bbmap.sh \\
+        ref=${fasta} \\
+        $options.args \\
+        threads=$task.cpus \\
+        -Xmx${task.memory.toGiga()}g
+
+    echo \$(bbversion.sh) > ${software}.version.txt
+    """
+}

modules/bbmap/index/meta.yml

@@ -0,0 +1,43 @@
+name: bbmap_index
+description: This module calls bbmap.sh to create an index from a fasta file, ready to be used by bbmap.sh in mapping mode.
+keywords:
+  - mapping
+  - index
+  - fasta
+tools:
+  - bbmap:
+      description: BBMap is a short read aligner, as well as various other bioinformatic tools.
+      homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
+      documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
+      tool_dev_url: None
+      doi: ""
+      licence: ['UC-LBL license (see package)']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing optional parameters to bbmap.sh
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: fasta
+      description: fasta formatted file with nucleotide sequences
+      pattern: "*.{fna,fa,fasta}"
+
+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}"
+  - db:
+      type: directory
+      description: Directory with index files
+      pattern: "ref"
+
+authors:
+  - "@daniellundin"

tests/config/pytest_modules.yml

@@ -30,6 +30,10 @@ bbmap/bbduk:
   - modules/bbmap/bbduk/**
   - tests/modules/bbmap/bbduk/**
 
+bbmap/index:
+  - modules/bbmap/index/**
+  - tests/modules/bbmap/index/**
+
 bcftools/concat:
   - modules/bcftools/concat/**
   - tests/modules/bcftools/concat/**
@@ -245,7 +249,7 @@ deeptools/plotprofile:
 delly/call:
   - modules/delly/call/**
   - tests/modules/delly/call/**
-  
+
 dragonflye:
   - modules/dragonflye/**
   - tests/modules/dragonflye/**

tests/modules/bbmap/index/main.nf

@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BBMAP_INDEX } from '../../../../modules/bbmap/index/main.nf' addParams( options: [:] )
+
+workflow test_bbmap_index {
+    
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    BBMAP_INDEX ( input )
+}

tests/modules/bbmap/index/test.yml

@@ -0,0 +1,12 @@
+## TODO nf-core: Please run the following command to build this file:
+#                nf-core modules create-test-yml bbmap/index
+- name: bbmap index
+  command: nextflow run ./tests/modules/bbmap/index -entry test_bbmap_index -c tests/config/nextflow.config
+  tags:
+    - bbmap
+    - bbmap/index
+  files:
+    - path: output/bbmap/ref/genome/1/chr1.chrom.gz
+      md5sum: fc20702f3378836f06d4104b9cd88918
+    - path: output/bbmap/ref/index/1/chr1_index_k13_c15_b1.block
+      md5sum: 9f0d9a7413c1d2c16cc24555b2381163