Diamond (#710)

* Added diamond

* minor tweaks & yml fix

* Fixed spacing issues due to failing lint

* Update modules/diamond/blastp/main.nf

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

* Update modules/diamond/blastp/main.nf

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

* Update modules/diamond/blastp/main.nf

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

* Update modules/diamond/blastp/main.nf

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

* Update modules/diamond/blastp/main.nf

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

* Update modules/diamond/blastx/main.nf

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

* Update modules/diamond/blastx/main.nf

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

* Update modules/diamond/blastx/main.nf

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

* Update modules/diamond/blastx/main.nf

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

* Update modules/diamond/makedb/main.nf

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

* Update modules/diamond/makedb/main.nf

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

* Update tests/modules/diamond/blastp/main.nf

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

* Update tests/modules/diamond/blastx/main.nf

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

* Update tests/modules/diamond/blastx/main.nf

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

* Update tests/modules/diamond/blastp/main.nf

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

* Update modules/diamond/blastp/meta.yml

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

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

modules/diamond/blastp/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/diamond/blastp/main.nf

@@ -0,0 +1,47 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process DIAMOND_BLASTP {
+    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']) }
+
+    // Dimaond is limited to v2.0.9 because there is not a
+    // singularity version higher than this at the current time.
+    conda (params.enable_conda ? "bioconda::diamond=2.0.9" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container 'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0'
+    } else {
+        container "quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0"
+    }
+
+    input:
+    tuple val(meta), path(fasta)
+    path  db
+
+    output:
+    tuple val(meta), path('*.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 "*.dmnd" | sed 's/.dmnd//'`
+
+    diamond \\
+        blastp \\
+        --threads $task.cpus \\
+        --db \$DB \\
+        --query $fasta \\
+        $options.args \\
+        --out ${prefix}.txt
+
+    echo \$(diamond --version 2>&1) | tail -n 1 | sed 's/^diamond version //' > ${software}.version.txt
+    """
+}

modules/diamond/blastp/meta.yml

@@ -0,0 +1,43 @@
+name: diamond_blastp
+description: Queries a DIAMOND database using blastp mode
+keywords:
+  - fasta
+  - diamond
+  - blastp
+  - DNA sequence
+tools:
+  - diamond:
+    description: Accelerated BLAST compatible local sequence aligner
+    homepage: https://github.com/bbuchfink/diamond
+    documentation: https://github.com/bbuchfink/diamond/wiki
+    tool_dev_url: https://github.com/bbuchfink/diamond
+    doi: "doi:10.1038/s41592-021-01101-x"
+    licence: ['GPL v3.0']
+
+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 query sequences
+        pattern: "*.{fa,fasta}"
+  - db:
+        type: directory
+        description: Directory containing the protein blast database
+        pattern: "*"
+
+output:
+  - txt:
+        type: file
+        description: File containing blastp hits
+        pattern: "*.{blastp.txt}"
+  - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+
+authors:
+  - "@spficklin"

modules/diamond/blastx/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/diamond/blastx/main.nf

@@ -0,0 +1,47 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process DIAMOND_BLASTX {
+    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']) }
+
+    // Dimaond is limited to v2.0.9 because there is not a
+    // singularity version higher than this at the current time.
+    conda (params.enable_conda ? "bioconda::diamond=2.0.9" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container 'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0'
+    } else {
+        container "quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0"
+    }
+
+    input:
+    tuple val(meta), path(fasta)
+    path  db
+
+    output:
+    tuple val(meta), path('*.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 "*.dmnd" | sed 's/.dmnd//'`
+
+    diamond \\
+        blastx \\
+        --threads $task.cpus \\
+        --db \$DB \\
+        --query $fasta \\
+        $options.args \\
+        --out ${prefix}.txt
+
+    echo \$(diamond --version 2>&1) | tail -n 1 | sed 's/^diamond version //' > ${software}.version.txt
+    """
+}

modules/diamond/blastx/meta.yml

@@ -0,0 +1,43 @@
+name: diamond_blastx
+description: Queries a DIAMOND database using blastx mode
+keywords:
+  - fasta
+  - diamond
+  - blastx
+  - DNA sequence
+tools:
+  - diamond:
+      description: Accelerated BLAST compatible local sequence aligner
+      homepage: https://github.com/bbuchfink/diamond
+      documentation: https://github.com/bbuchfink/diamond/wiki
+      tool_dev_url: https://github.com/bbuchfink/diamond
+      doi: "doi:10.1038/s41592-021-01101-x"
+      licence: ['GPL v3.0']
+
+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 query sequences
+        pattern: "*.{fa,fasta}"
+    - db:
+        type: directory
+        description: Directory containing the nucelotide blast database
+        pattern: "*"
+
+output:
+    - txt:
+        type: file
+        description: File containing blastx hits
+        pattern: "*.{blastx.txt}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+
+authors:
+  - "@spficklin"

modules/diamond/makedb/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/diamond/makedb/main.nf

@@ -0,0 +1,42 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process DIAMOND_MAKEDB {
+    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), meta:[:], publish_by_meta:[]) }
+
+    // Dimaond is limited to v2.0.9 because there is not a
+    // singularity version higher than this at the current time.
+    conda (params.enable_conda ? 'bioconda::diamond=2.0.9' : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container 'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0'
+    } else {
+        container 'quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0'
+    }
+
+    input:
+    path fasta
+
+    output:
+    path "${fasta}.dmnd", emit: db
+    path '*.version.txt', emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    """
+    diamond \\
+        makedb \\
+        --threads $task.cpus \\
+        --in  $fasta \\
+        -d $fasta \\
+        $options.args
+
+    echo \$(diamond --version 2>&1) | tail -n 1 | sed 's/^diamond version //' > ${software}.version.txt
+    """
+}

modules/diamond/makedb/meta.yml

@@ -0,0 +1,34 @@
+name: diamond_makedb
+description: Builds a DIAMOND database
+keywords:
+  - fasta
+  - diamond
+  - index
+  - database
+tools:
+  - diamond:
+    description: Accelerated BLAST compatible local sequence aligner
+    homepage: https://github.com/bbuchfink/diamond
+    documentation: https://github.com/bbuchfink/diamond/wiki
+    tool_dev_url: https://github.com/bbuchfink/diamond
+    doi: "doi:10.1038/s41592-021-01101-x"
+    licence: ['GPL v3.0']
+
+input:
+  - fasta:
+      type: file
+      description: Input fasta file
+      pattern: "*.{fa,fasta}"
+
+output:
+  - db:
+      type: file
+      description: File of the indexed DIAMOND database
+      pattern: "*.{dmnd}"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+
+authors:
+  - "@spficklin"

tests/config/pytest_modules.yml

@@ -286,6 +286,18 @@ delly/call:
   - modules/delly/call/**
   - tests/modules/delly/call/**
 
+diamond/blastx:
+  - modules/diamond/blastx/**
+  - tests/modules/diamond/blastx/**
+
+diamond/blastp:
+  - modules/diamond/blastp/**
+  - tests/modules/diamond/blastp/**
+
+diamond/makedb:
+  - modules/diamond/makedb/**
+  - tests/modules/diamond/makedb/**
+
 dragonflye:
   - modules/dragonflye/**
   - tests/modules/dragonflye/**

tests/modules/diamond/blastp/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DIAMOND_MAKEDB } from '../../../../modules/diamond/makedb/main.nf' addParams( options: [:]                           )
+include { DIAMOND_BLASTP } from '../../../../modules/diamond/blastp/main.nf' addParams( options: [ suffix: '.diamond_blastp' ] )
+
+workflow test_diamond_blastp {
+
+    db = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+    fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
+
+    DIAMOND_MAKEDB ( db )
+    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db )
+}

tests/modules/diamond/blastp/test.yml

@@ -0,0 +1,8 @@
+- name: diamond blastp
+  command: nextflow run ./tests/modules/diamond/blastp -entry test_diamond_blastp -c tests/config/nextflow.config
+  tags:
+      - diamond
+      - diamond/blastp
+  files:
+      - path: ./output/diamond/test.diamond_blastp.txt
+        md5sum: 3ca7f6290c1d8741c573370e6f8b4db0

tests/modules/diamond/blastx/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DIAMOND_MAKEDB } from '../../../../modules/diamond/makedb/main.nf' addParams( options: [:]                           )
+include { DIAMOND_BLASTX } from '../../../../modules/diamond/blastx/main.nf' addParams( options: [ suffix: '.diamond_blastx' ] )
+
+workflow test_diamond_blastx {
+
+    db = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+    fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
+
+    DIAMOND_MAKEDB ( db )
+    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db )
+}

tests/modules/diamond/blastx/test.yml

@@ -0,0 +1,8 @@
+- name: diamond blastx
+  command: nextflow run ./tests/modules/diamond/blastx -entry test_diamond_blastx -c tests/config/nextflow.config
+  tags:
+      - diamond
+      - diamond/blastx
+  files:
+      - path: ./output/diamond/test.diamond_blastx.txt
+        md5sum: d41d8cd98f00b204e9800998ecf8427e

tests/modules/diamond/makedb/main.nf

@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DIAMOND_MAKEDB } from '../../../../modules/diamond/makedb/main.nf' addParams( options: [:] )
+
+workflow test_diamond_makedb {
+
+    input = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    DIAMOND_MAKEDB ( input )
+}

tests/modules/diamond/makedb/test.yml

@@ -0,0 +1,8 @@
+- name: diamond makedb test_diamond_makedb
+  command: nextflow run ./tests/modules/diamond/makedb -entry test_diamond_makedb -c tests/config/nextflow.config
+  tags:
+    - diamond
+    - diamond/makedb
+  files:
+    - path: output/diamond/genome.fasta.dmnd
+      md5sum: 2447fb376394c20d43ea3aad2aa5d15d