Add Racon module to nf-core/modules (#949)

* add racon

* add racon

* add racon

* add racon module

* add racon module

* edit racon module

* edit racon module

* edit racon module

* edit racon module

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>

modules/racon/functions.nf

@@ -0,0 +1,78 @@
+//
+//  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()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${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"
+    }
+}

modules/racon/main.nf

@@ -0,0 +1,45 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process RACON {
+    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::racon=1.4.20" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/racon:1.4.20--h9a82719_1"
+    } else {
+        container "quay.io/biocontainers/racon:1.4.20--h9a82719_1"
+    }
+
+    input:
+    tuple val(meta), path(reads), path(assembly), path(paf)
+
+    output:
+    tuple val(meta), path('*_assembly_consensus.fasta.gz') , emit: improved_assembly
+    path "versions.yml"          , emit: versions
+
+    script:
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    racon -t "${task.cpus}" \\
+        "${reads}" \\
+        "${paf}" \\
+        $options.args \\
+        "${assembly}" > \\
+        ${prefix}_assembly_consensus.fasta
+
+    gzip -n ${prefix}_assembly_consensus.fasta
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$( racon --version 2>&1 | sed 's/^.*v//' )
+    END_VERSIONS
+    """
+}

modules/racon/meta.yml

@@ -0,0 +1,52 @@
+name: racon
+description: Consensus module for raw de novo DNA assembly of long uncorrected reads
+keywords:
+  - assembly
+  - pacbio
+  - nanopore
+  - polish
+tools:
+  - racon:
+      description: Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.
+      homepage: https://github.com/lbcb-sci/racon
+      documentation: https://github.com/lbcb-sci/racon
+      tool_dev_url: https://github.com/lbcb-sci/racon
+      doi: https://doi.org/10.1101/gr.214270.116
+      licence: ['MIT']
+
+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. Racon expects single end reads
+      pattern: "*.{fastq,fastq.gz,fq,fq.gz}"
+  - assembly:
+      type: file
+      description: Genome assembly to be improved
+      pattern: "*.{fasta,fa}"
+  - paf:
+      type: file
+      description: Alignment in PAF format
+      pattern: "*.paf"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - improved_assembly:
+      type: file
+      description: Improved genome assembly
+      pattern: "*_assembly_consensus.fasta.gz"
+
+authors:
+  - "@avantonder"

tests/config/pytest_modules.yml

@@ -923,6 +923,10 @@ quast:
   - modules/quast/**
   - tests/modules/quast/**
 
+racon:
+  - modules/racon/**
+  - tests/modules/racon/**
+
 rapidnj:
   - modules/rapidnj/**
   - tests/modules/rapidnj/**

tests/config/test_data.config

@@ -11,6 +11,7 @@ params {
                 genome_gff3                                    = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3"
                 genome_gff3_gz                                 = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3.gz"
                 genome_gtf                                     = "${test_data_dir}/genomics/sarscov2/genome/genome.gtf"
+                genome_paf                                     = "${test_data_dir}/genomics/sarscov2/genome/genome.paf"
                 genome_sizes                                   = "${test_data_dir}/genomics/sarscov2/genome/genome.sizes"
                 transcriptome_fasta                            = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.fasta"
                 transcriptome_paf                              = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.paf"
@@ -243,6 +244,7 @@ params {
         'bacteroides_fragilis'{
             'genome' {
                 genome_fna_gz                   = "${test_data_dir}/genomics/bacteroides_fragilis/genome/genome.fna.gz"
+                genome_paf                      = "${test_data_dir}/genomics/bacteroides_fragilis/genome/genome.paf"
             }
             'illumina' {
                 test1_contigs_fa_gz             = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz"
@@ -253,7 +255,8 @@ params {
             }
             'nanopore' {
                 test_fastq_gz                   = "${test_data_dir}/genomics/bacteroides_fragilis/nanopore/fastq/test.fastq.gz"
+                overlap_paf                     = "${test_data_dir}/genomics/bacteroides_fragilis/nanopore/overlap.paf"
             }
-        }
+        }    
     }
 }

tests/modules/minimap2/align/test.yml

@@ -14,4 +14,4 @@
     - minimap2/align
   files:
     - path: ./output/minimap2/test.paf
-      md5sum: 5e7b55a26bf0ea3a2843423d3e0b9a28
+      md5sum: 5e7b55a26bf0ea3a2843423d3e0b9a28

tests/modules/racon/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RACON } from '../../../modules/racon/main.nf' addParams( options: [:] )
+
+workflow test_racon {
+    input = [ [ id:'test', single_end:true ], // meta map
+              file(params.test_data['bacteroides_fragilis']['nanopore']['test_fastq_gz'], checkIfExists: true),
+              file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true),
+              file(params.test_data['bacteroides_fragilis']['genome']['genome_paf'], checkIfExists: true)
+            ]
+
+    RACON ( input )
+}

tests/modules/racon/test.yml

@@ -0,0 +1,7 @@
+- name: racon test_racon
+  command: nextflow run tests/modules/racon -entry test_racon -c tests/config/nextflow.config
+  tags:
+    - racon
+  files:
+    - path: output/racon/test_assembly_consensus.fasta.gz
+      md5sum: 96a0ba94c6154f6f37b5a76a0207eb6f