Merge remote-tracking branch 'upstream/master' into bedtools_getfasta

.github/filters.yml

@@ -4,27 +4,27 @@ bandage_image:
 
 bcftools_bgzip:
   - software/bcftools/bgzip/**
-  - tests/software/bcftools/bgzip**
+  - tests/software/bcftools/bgzip/**
 
 bcftools_consensus:
   - software/bcftools/consensus/**
-  - tests/software/bcftools/consensus**
+  - tests/software/bcftools/consensus/**
 
 bcftools_filter:
   - software/bcftools/filter/**
-  - tests/software/bcftools/filter**
+  - tests/software/bcftools/filter/**
 
 bcftools_isec:
   - software/bcftools/isec/**
-  - tests/software/bcftools/isec**
+  - tests/software/bcftools/isec/**
 
 bcftools_stats:
   - software/bcftools/stats/**
-  - tests/software/bcftools/stats**
+  - tests/software/bcftools/stats/**
 
 bcftools_tabix:
   - software/bcftools/tabix/**
-  - tests/software/bcftools/tabix**
+  - tests/software/bcftools/tabix/**
 
 bedtools_complement:
   - software/bedtools/complement/**
@@ -60,7 +60,11 @@ bedtools_sort:
 
 blast_makeblastdb:
   - software/blast/makeblastdb/**
-  - tests/software/blast/makeblastdb**
+  - tests/software/blast/makeblastdb/**
+
+blast_blastn:
+  - software/blast/blastn/**
+  - tests/software/blast/blastn/**
 
 bowtie:
   - software/bowtie/build/**

software/blast/blastn/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/blastn/main.nf

@@ -0,0 +1,42 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process BLAST_BLASTN {
+    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::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:
+    tuple val(meta), path(fasta)
+    path  db
+
+    output:
+    tuple val(meta), path('*.blastn.txt'), emit: txt
+    path '*.version.txt'                 , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    DB=`find -L ./ -name "*.ndb" | sed 's/.ndb//'`
+    blastn \\
+        -num_threads $task.cpus \\
+        -db \$DB \\
+        -query $fasta \\
+        $options.args \\
+        -out ${prefix}.blastn.txt
+    echo \$(blastn -version 2>&1) | sed 's/^.*blastn: //; s/ .*\$//' > ${software}.version.txt
+    """
+}

software/blast/blastn/meta.yml

@@ -0,0 +1,61 @@
+name: blast_blastn
+description: Queries a BLAST DNA database
+keywords:
+    - fasta
+    - blast
+    - blastn
+    - DNA sequence
+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:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - fasta:
+        type: file
+        description: Input fasta file containing queries sequences
+        pattern: "*.{fa,fasta}"
+    - db:
+        type: directory
+        description: Directory containing blast database
+        pattern: "*"
+output:
+    - txt:
+        type: file
+        description: File containing blastn hits
+        pattern: "*.{blastn.txt}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@joseespinosa"
+    - "@drpatelh"

tests/software/blast/blastn/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BLAST_MAKEBLASTDB } from '../../../../software/blast/makeblastdb/main.nf' addParams( options: ['args': '-dbtype nucl'] )
+include { BLAST_BLASTN } from '../../../../software/blast/blastn/main.nf' addParams( options: [:] )
+
+workflow test_blast_blastn {
+
+    def input = []
+    input = [ file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) ]
+
+    BLAST_MAKEBLASTDB (input)
+    BLAST_BLASTN ([ [id:'test'], input ], BLAST_MAKEBLASTDB.out.db)
+}

tests/software/blast/blastn/test.yml

@@ -0,0 +1,22 @@
+- name: blast_blastn
+  command: nextflow run ./tests/software/blast/blastn -entry test_blast_blastn -c tests/config/nextflow.config
+  tags:
+    - blast
+    - blast_blastn
+  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
+    - path: output/blast/test.blastn.txt
+      should_exist: true