started adding quast modules

software/quast/quast_noref/functions.nf

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+/*
+ * -----------------------------------------------------
+ *  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/quast/quast_noref/main.nf

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+// 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

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+name: quast
+description: Quality Assessment Tool for Genome Assemblies
+keywords:
+  - quast
+  - assembly
+  - quality
+tools:
+  - star:
+      description: |
+        QUAST calculate 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: map
+      description: |
+        Groovy Map containing sample information
+
+output:
+  - report:
+      type: file
+      description: The lineage report
+      pattern: "{prefix}.lineage_report.csv"
+
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+
+authors:
+  - "@drpatelh"
+  - "@kevinmenden"

software/quast/quast_ref/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  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/quast/quast_ref/main.nf

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+// 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
+    path fasta
+    path gff
+
+    output:
+    path "${prefix}"    , emit: results
+    path '*.tsv'        , emit: tsv
+    path '*.version.txt', emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    prefix       = options.suffix ?: software
+    def features = params.gff ? "--features $gff" : ''
+    """
+    quast.py \\
+        --output-dir $prefix \\
+        -r $fasta \\
+        $features \\
+        --threads $task.cpus \\
+        $options.args \\
+        ${consensus.join(' ')}
+    ln -s ${prefix}/report.tsv
+    echo \$(quast.py --version 2>&1) | sed 's/^.*QUAST v//; s/ .*\$//' > ${software}.version.txt
+    """
+}

software/quast/quast_ref/meta.yml

@@ -0,0 +1,61 @@
+name: quast
+description: Quality Assessment Tool for Genome Assemblies
+keywords:
+  - quast
+  - assembly
+  - quality
+tools:
+  - star:
+      description: |
+        QUAST calculate 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: map
+      description: |
+        Groovy Map containing sample information
+  - fasta:
+      type: file
+      description: |
+        The genome assembly to be evaluated
+  - gff:
+      type: file
+      description: The genome GFF file
+
+output:
+  - report:
+      type: file
+      description: The lineage report
+      pattern: "{prefix}.lineage_report.csv"
+
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+
+authors:
+  - "@drpatelh"
+  - "@kevinmenden"

tests/software/quast/main.nf

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+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { QUAST as QUAST_NOREF } from '../../../software/quast/quast_noref/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)
+
+    QUAST_REF( consensus, fasta, gff )
+}