Add artic guppyplex (#455)

* Adding artic guppyplex module

* Adding guppyplex tests

* Fix tests

* Correcting typo

* Fix lint

* Fix test

* Missing description

* Missing descriptions

* Update functions to last version as suggested

* Bump newest version of nanoplot

software/artic/guppyplex/functions.nf

@@ -0,0 +1,70 @@
+/*
+ * -----------------------------------------------------
+ *  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"
+        }
+    }
+}

software/artic/guppyplex/main.nf

@@ -0,0 +1,41 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process ARTIC_GUPPYPLEX {
+    tag "$meta.id"
+    label 'process_high'
+    publishDir "${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']) }
+
+    conda (params.enable_conda ? "bioconda::artic=1.2.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/artic:1.2.1--py_0"
+    } else {
+        container "quay.io/biocontainers/artic:1.2.1--py_0"
+    }
+
+    input:
+    tuple val(meta), path(fastq_dir)
+
+    output:
+    tuple val(meta), path("*.fastq.gz"), emit: fastq
+    path  "*.version.txt"              , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    artic \\
+        guppyplex \\
+        $options.args \\
+        --directory $fastq_dir \\
+        --output ${prefix}.fastq
+
+    pigz -p $task.cpus *.fastq
+    echo \$(artic --version 2>&1) | sed 's/^.*artic //; s/ .*\$//' > ${software}.version.txt
+    """
+}

software/artic/guppyplex/meta.yml

@@ -0,0 +1,44 @@
+name: artic_guppyplex
+description: Aggregates fastq files with demultiplexed reads
+keywords:
+  - artic
+  - aggregate
+  - demultiplexed reads
+tools:
+  - artic:
+      description: ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore
+      homepage: https://artic.readthedocs.io/en/latest/
+      documentation: https://artic.readthedocs.io/en/latest/
+      tool_dev_url: https://github.com/artic-network/fieldbioinformatics
+      doi: ""
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fastq_dir:
+      type: directory
+      description: Directory containing the fastq files with demultiplexed reads
+      pattern: "*"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fastq:
+      type: file
+      description: Aggregated FastQ files
+      pattern: "*.{fastq.gz}"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+
+authors:
+  - "@joseespinosa"
+  - "@drpatelh"

software/nanoplot/main.nf

@@ -11,11 +11,11 @@ process NANOPLOT {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::nanoplot=1.32.1" : null)
+    conda (params.enable_conda ? "bioconda::nanoplot=1.36.1" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/nanoplot:1.32.1--py_0"
+        container "https://depot.galaxyproject.org/singularity/nanoplot:1.36.1--pyhdfd78af_0"
     } else {
-        container "quay.io/biocontainers/nanoplot:1.32.1--py_0"
+        container "quay.io/biocontainers/nanoplot:1.36.1--pyhdfd78af_0"
     }
 
     input:

software/nanoplot/meta.yml

@@ -26,7 +26,7 @@ input:
     - summary_txt:
         type: file
         description: |
-            List of sequenicng_summary.txt files from running basecalling.
+            List of sequencing_summary.txt files from running basecalling.
 output:
     - meta:
         type: map

tests/config/pytest_software.yml

@@ -10,6 +10,10 @@ allelecounter:
   - software/allelecounter/**
   - tests/software/allelecounter/**
 
+artic/guppyplex:
+  - software/artic/guppyplex/**
+  - tests/software/artic/guppyplex/**
+
 bandage/image:
   - software/bandage/image/**
   - tests/software/bandage/image/**

tests/software/artic/guppyplex/main.nf

@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ARTIC_GUPPYPLEX } from '../../../../software/artic/guppyplex/main.nf' addParams( options: [:] )
+
+process STAGE_FASTQ_DIR {
+    input:
+    tuple val(meta), path(fastq_file)
+
+    output:
+    tuple val(meta), path('fastq'), emit: fastq_dir
+
+    script:
+    """
+    mkdir fastq
+    mv ${fastq_file} fastq
+    """
+}
+
+workflow test_artic_guppyplex {
+
+    input =  [ [ id:'test' ],
+               file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
+
+    STAGE_FASTQ_DIR ( input )
+
+    ARTIC_GUPPYPLEX ( STAGE_FASTQ_DIR.out.fastq_dir )
+}

tests/software/artic/guppyplex/test.yml

@@ -0,0 +1,7 @@
+- name: artic guppyplex
+  command: nextflow run tests/software/artic/guppyplex -entry test_artic_guppyplex -c tests/config/nextflow.config
+  tags:
+    - artic
+    - artic/guppyplex
+  files:
+    - path: output/artic/test.fastq.gz