Add pycoqc module (#424)

* Add pycoqc module

* Adding pycoqc module tests

* Update pycoqc wilth new functions.nf

* Update tests to check for json report content

software/pycoqc/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/pycoqc/main.nf

@@ -0,0 +1,40 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process PYCOQC {
+    tag "$summary"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
+
+    conda (params.enable_conda ? "bioconda::pycoqc=2.5.2" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/pycoqc:2.5.2--py_0"
+    } else {
+        container "quay.io/biocontainers/pycoqc:2.5.2--py_0"
+    }
+
+    input:
+    path summary
+
+    output:
+    path "*.html"        , emit: html
+    path "*.json"        , emit: json
+    path  "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    """
+    pycoQC \\
+        $options.args \\
+        -f $summary \\
+        -o pycoqc.html \\
+        -j pycoqc.json
+
+    echo \$(pycoQC --version 2>&1) | sed 's/^.*pycoQC v//; s/ .*\$//' > ${software}.version.txt
+    """
+}

software/pycoqc/meta.yml

@@ -0,0 +1,48 @@
+name: pycoqc
+description: write your description here
+keywords:
+  - qc
+  - quality control
+  - sequencing
+  - nanopore
+tools:
+  - pycoqc:
+      description: PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data
+      homepage: https://github.com/tleonardi/pycoQC
+      documentation: https://tleonardi.github.io/pycoQC/
+      tool_dev_url: https://github.com/tleonardi/pycoQC
+      doi: "10.21105/joss.01236"
+      licence: ['GNU General Public v3 (GPL v3)']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - summary:
+      type: file
+      description: sequencing summary file
+      pattern: "*.{txt}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - html:
+      type: file
+      description: Results in HTML format
+  - json:
+      type: file
+      description: Results in JSON format
+      pattern: "*.{json}"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+
+authors:
+  - "@joseespinosa"
+  - "@drpatelh"

tests/config/pytest_software.yml

@@ -386,6 +386,10 @@ prokka:
   - software/prokka/**
   - tests/software/prokka/**
 
+pycoqc:
+  - software/pycoqc/**
+  - tests/software/pycoqc/**
+
 qualimap/bamqc:
   - software/qualimap/bamqc/**
   - tests/software/qualimap/bamqc/**

tests/software/pycoqc/main.nf

@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PYCOQC } from '../../../software/pycoqc/main.nf' addParams ( options: ['args' : '--min_pass_qual 0'] )
+
+workflow test_pycoqc {
+
+    input = [ file(params.test_data['sarscov2']['nanopore']['test_sequencing_summary'], checkIfExists: true) ]
+
+    PYCOQC ( input )
+}

tests/software/pycoqc/test.yml

@@ -0,0 +1,11 @@
+- name: pycoqc
+  command: nextflow run ./tests/software/pycoqc -entry test_pycoqc -c tests/config/nextflow.config
+  tags:
+    - pycoqc
+  files:
+    - path: output/pycoqc/pycoqc.json
+      contains:
+        - '"reads_number": 100,'
+        - '"bases_number": 1160,'
+        - '"N50": 12,'
+    - path: output/pycoqc/pycoqc.html