Merge pull request #159 from JoseEspinosa/blast_makeblastdb

Add blast makeblastdb module

.github/filters.yml

@@ -54,6 +54,10 @@ bedtools_sort:
   - software/bedtools/sort/**
   - tests/software/bedtools/sort/**
 
+blast_makeblastdb:
+  - software/blast/makeblastdb/**
+  - tests/software/blast/makeblastdb**
+
 bowtie:
   - software/bowtie/build/**
   - tests/software/bowtie/build/**

software/blast/makeblastdb/functions.nf

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

software/blast/makeblastdb/main.nf

@@ -0,0 +1,38 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process BLAST_MAKEBLASTDB {
+    tag "$fasta"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+
+    conda (params.enable_conda ? 'bioconda::blast=2.10.1' : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container 'https://depot.galaxyproject.org/singularity/blast:2.10.1--pl526he19e7b1_3'
+    } else {
+        container 'quay.io/biocontainers/blast:2.10.1--pl526he19e7b1_3'
+    }
+
+    input:
+    path fasta
+
+    output:
+    path 'blast_db'     , emit: db
+    path '*.version.txt', emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    """
+    makeblastdb \\
+        -in $fasta \\
+        $options.args
+    mkdir blast_db
+    mv ${fasta}* blast_db
+    echo \$(blastn -version 2>&1) | sed 's/^.*blastn: //; s/ .*\$//' > ${software}.version.txt
+    """
+}

software/blast/makeblastdb/meta.yml

@@ -0,0 +1,51 @@
+name: blast_makeblastdb
+description: Builds a BLAST database
+keywords:
+    - fasta
+    - blast
+    - database
+tools:
+    - blast:
+          description: |
+              BLAST finds regions of similarity between biological sequences.
+          homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi
+          documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs
+          doi: 10.1016/S0022-2836(05)80360-2
+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:
+    - fasta:
+        type: file
+        description: Input fasta file
+        pattern: "*.{fa,fasta}"
+output:
+    - db:
+          type: directory
+          description: Output directory containing blast database files
+          pattern: "*"
+    - version:
+          type: file
+          description: File containing software version
+          pattern: "*.{version.txt}"
+authors:
+    - "@joseespinosa"
+    - "@drpatelh"

tests/software/blast/makeblastdb/main.nf

@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BLAST_MAKEBLASTDB } from '../../../../software/blast/makeblastdb/main.nf' addParams( options: ['args': '-dbtype nucl'] )
+
+workflow test_blast_makeblastdb {
+    def input = []
+    input =  [ file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) ]
+
+    BLAST_MAKEBLASTDB( input )
+}

tests/software/blast/makeblastdb/test.yml

@@ -0,0 +1,20 @@
+- name: blast_makeblastdb
+  command: nextflow run ./tests/software/blast/makeblastdb -entry test_blast_makeblastdb -c tests/config/nextflow.config
+  tags:
+    - blast
+    - blast_makeblastdb
+  files:
+    - path: output/blast/blast_db/NC_010473.fa
+      md5sum: ad277e6b3da5dcf9fccfcd3a55fcec8e
+    - path: output/blast/blast_db/NC_010473.fa.ndb
+      md5sum: 5fc66e1a2b3b38966eb40ed15642ba3e
+    - path: output/blast/blast_db/NC_010473.fa.nhr
+      md5sum: 41702062ff7cce21e0649864013fad73
+    - path: output/blast/blast_db/NC_010473.fa.nin
+      should_exist: true
+    - path: output/blast/blast_db/NC_010473.fa.not
+      md5sum: 1e53e9d08f1d23af0299cfa87478a7bb
+    - path: output/blast/blast_db/NC_010473.fa.nsq
+      md5sum: 8e2d0c3fc02a8c2c886bafb73bdd8a89
+    - path: output/blast/blast_db/NC_010473.fa.ntf
+      md5sum: 1f6027d443e67a98ad0edc2d39971b0c