From 38b450d0be865af4f60dd4674a4fc47ddbf1e6e1 Mon Sep 17 00:00:00 2001
From: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Date: Tue, 16 Mar 2021 09:54:29 +0000
Subject: [PATCH] hifiasm copied from fastqc

---
 software/hifiasm/functions.nf | 59 ++++++++++++++++++++++++++++
 software/hifiasm/main.nf      | 47 +++++++++++++++++++++++
 software/hifiasm/meta.yml     | 72 +++++++++++++++++++++++++++++++++++
 3 files changed, 178 insertions(+)
 create mode 100644 software/hifiasm/functions.nf
 create mode 100644 software/hifiasm/main.nf
 create mode 100644 software/hifiasm/meta.yml

diff --git a/software/hifiasm/functions.nf b/software/hifiasm/functions.nf
new file mode 100644
index 00000000..d25eea86
--- /dev/null
+++ b/software/hifiasm/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)}/$args.filename"
+        }
+    }
+}
diff --git a/software/hifiasm/main.nf b/software/hifiasm/main.nf
new file mode 100644
index 00000000..4e847876
--- /dev/null
+++ b/software/hifiasm/main.nf
@@ -0,0 +1,47 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process FASTQC {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0"
+    } else {
+        container "quay.io/biocontainers/fastqc:0.11.9--0"
+    }
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path("*.html"), emit: html
+    tuple val(meta), path("*.zip") , emit: zip
+    path  "*.version.txt"          , emit: version
+
+    script:
+    // Add soft-links to original FastQs for consistent naming in pipeline
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
+    if (meta.single_end) {
+        """
+        [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
+        fastqc $options.args --threads $task.cpus ${prefix}.fastq.gz
+        fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt
+        """
+    } else {
+        """
+        [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
+        [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
+        fastqc $options.args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
+        fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt
+        """
+    }
+}
diff --git a/software/hifiasm/meta.yml b/software/hifiasm/meta.yml
new file mode 100644
index 00000000..413aad8d
--- /dev/null
+++ b/software/hifiasm/meta.yml
@@ -0,0 +1,72 @@
+name: fastqc
+description: Run FastQC on sequenced reads
+keywords:
+    - quality control
+    - qc
+    - adapters
+    - fastq
+tools:
+    - fastqc:
+        description: |
+            FastQC gives general quality metrics about your reads.
+            It provides information about the quality score distribution
+            across your reads, the per base sequence content (%A/C/G/T).
+            You get information about adapter contamination and other
+            overrepresented sequences.
+        homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
+        documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
+params:
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$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:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: |
+            List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+            respectively.
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - html:
+        type: file
+        description: FastQC report
+        pattern: "*_{fastqc.html}"
+    - zip:
+        type: file
+        description: FastQC report archive
+        pattern: "*_{fastqc.zip}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@drpatelh"
+    - "@grst"
+    - "@ewels"
+    - "@FelixKrueger"