refactored quast module

software/quast/main.nf

@@ -21,7 +21,9 @@ process QUAST {
     input:
     path consensus
     path fasta
+    val use_fasta
     path gff
+    val use_gff
 
     output:
     path "${prefix}"    , emit: results
@@ -29,14 +31,15 @@ process QUAST {
     path '*.version.txt', emit: version
 
     script:
-    def software = getSoftwareName(task.process)
+    def software  = getSoftwareName(task.process)
-    prefix       = options.suffix ?: software
+    prefix        = options.suffix ?: software
-    def features = params.gff ? "--features $gff" : ''
+    def features  = use_gff ? "--features $gff" : ''
+    def reference = use_fasta ? "-r $fasta" : ''
     """
     quast.py \\
         --output-dir $prefix \\
-        -r $fasta \\
+        ${reference} \\
-        $features \\
+        ${features} \\
         --threads $task.cpus \\
         $options.args \\
         ${consensus.join(' ')}

software/quast/meta.yml

@@ -1,4 +1,4 @@
-name: quast_reference
+name: quast
 description: Quality Assessment Tool for Genome Assemblies
 keywords:
   - quast
@@ -40,10 +40,16 @@ input:
   - fasta:
       type: file
       description: |
-        The genome assembly to be evaluated
+        The genome assembly to be evaluated. Has to contain at least a non-empty string dummy value.
+  - use_fasta:
+      type: boolean
+      description: Whether to use a fasta reference
   - gff:
       type: file
-      description: The genome GFF file
+      description: The genome GFF file. Has to contain at least a non-empty string dummy value.
+  - use_gff:
+      type: boolean
+      description: Whether to use a gff reference
 
 output:
   - quast:

software/quast/quast_noref/main.nf

@@ -1,41 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-def options    = initOptions(params.options)
-
-process QUAST {
-    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::quast=5.0.2' : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container 'https://depot.galaxyproject.org/singularity/quast:5.0.2--py37pl526hb5aa323_2'
-    } else {
-        container 'quay.io/biocontainers/quast:5.0.2--py37pl526hb5aa323_2'
-    }
-
-    input:
-    path consensus
-
-    output:
-    path "${prefix}"    , emit: results
-    path '*.tsv'        , emit: tsv
-    path '*.version.txt', emit: version
-
-    script:
-    def software         = getSoftwareName(task.process)
-    prefix               = options.suffix ?: software
-    """
-    quast.py \\
-        --output-dir $prefix \\
-        --threads $task.cpus \\
-        $options.args \\
-        $consensus
-    ln -s ${prefix}/report.tsv
-    echo \$(quast.py --version 2>&1) | sed 's/^.*QUAST v//; s/ .*\$//' > ${software}.version.txt
-    """
-}

software/quast/quast_noref/meta.yml

@@ -1,55 +0,0 @@
-name: quast
-description: Quality Assessment Tool for Genome Assemblies
-keywords:
-  - quast
-  - assembly
-  - quality
-tools:
-  - quast:
-      description: |
-        QUAST calculates quality metrics for genome assemblies
-      homepage: http://bioinf.spbau.ru/quast
-      doi:
-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:
-  - consensus:
-      type: file
-      description: |
-        Fasta file containing the assembly of interest
-
-output:
-  - results:
-      type: file
-      description: The lineage report
-      pattern: "{prefix}.lineage_report.csv"
-  - tsv:
-
-  - version:
-      type: file
-      description: File containing software version
-      pattern: "*.{version.txt}"
-
-authors:
-  - "@drpatelh"
-  - "@kevinmenden"

software/quast/quast_ref/functions.nf

@@ -1,59 +0,0 @@
-/*
- * -----------------------------------------------------
- *  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"
-        }
-    }
-}

tests/software/quast/main.nf

@@ -2,19 +2,24 @@
 
 nextflow.enable.dsl = 2
 
-include { QUAST as QUAST_NOREF } from '../../../software/quast/quast_noref/main.nf' addParams(options: [:])
+include { QUAST }   from '../../../software/quast/main.nf'   addParams(options: [:])
-include { QUAST as QUAST_REF }   from '../../../software/quast/quast_ref/main.nf'   addParams(options: [:])
-
-workflow test_quast_noref {
-    consensus = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
-
-    QUAST_NOREF( consensus )
-}
 
 workflow test_quast_ref {
     consensus = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
     gff = file("${launchDir}/tests/data/gff/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true)
     fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
+    def use_fasta = true
+    def use_gtf = true
 
-    QUAST_REF( consensus, fasta, gff )
+    QUAST( consensus, fasta, use_fasta, gff, use_gtf)
+}
+
+workflow test_quast_noref {
+    consensus = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
+    gff = file('gff_dummy')
+    fasta = file('fasta_dummy')
+    def use_fasta = false
+    def use_gtf = false
+
+    QUAST( consensus, fasta, use_fasta, gff, use_gtf)
 }