Rewritten module fgbio/fastqtobam (#916)

* added template for fastqtobam

* porting old code into new template

* update with missing getprocessname function

* test completed - updating all

* fixed linting issues

* improved reading

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

modules/fgbio/fastqtobam/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+    // Do not publish versions.yml unless running from pytest workflow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/fgbio/fastqtobam/main.nf

@@ -0,0 +1,51 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process FGBIO_FASTQTOBAM {
+    tag "$meta.id"
+    label 'process_low'
+    publishDir "${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::fgbio=1.4.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/fgbio:1.4.0--hdfd78af_0"
+    } else {
+        container "quay.io/biocontainers/fgbio:1.4.0--hdfd78af_0"
+    }
+
+    input:
+    tuple val(meta), path(reads)
+    val(read_structure)
+
+    output:
+    tuple val(meta), path("*_umi_converted.bam"), emit: umibam
+    path "versions.yml"                         , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+
+    """
+    mkdir tmpFolder
+
+    fgbio \\
+        --tmp-dir=${PWD}/tmpFolder \\
+        FastqToBam \\
+        -i $reads \\
+        -o "${prefix}_umi_converted.bam" \\
+        --read-structures $read_structure \\
+        --sample $meta.id \\
+        --library $meta.id \\
+        $options.args
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$( echo \$(fgbio --version 2>&1 | tr -d '[:cntrl:]' ) | sed -e 's/^.*Version: //;s/\\[.*\$//')
+    END_VERSIONS
+    """
+}

modules/fgbio/fastqtobam/meta.yml

@@ -0,0 +1,47 @@
+name: fgbio_fastqtobam
+description: |
+      Using the FGBIO tools, converts FASTQ files sequenced with UMIs into BAM files, moving the UMI barcode into the RX field of the BAM file
+keywords:
+  - fastqtobam
+  - fgbio
+tools:
+  - fgbio:
+      description: A set of tools for working with genomic and high throughput sequencing data, including UMIs
+      homepage: http://fulcrumgenomics.github.io/fgbio/
+      documentation: http://fulcrumgenomics.github.io/fgbio/tools/latest/
+      tool_dev_url: https://github.com/fulcrumgenomics/fgbio
+      doi: ""
+      licence: ['MIT']
+
+input:
+  - reads:
+      type: file
+      description: pair of reads to be converted into BAM file
+      pattern: "*.{fastq.gz}"
+
+  - read_structure:
+      type: string
+      description: |
+                  A read structure should always be provided for each of the fastq files.
+                  If single end, the string will contain only one structure (i.e. "2M11S+T"), if paired-end the string
+                  will contain two structures separated by a blank space (i.e. "2M11S+T 2M11S+T").
+                  If the read does not contain any UMI, the structure will be +T (i.e. only template of any length).
+                  https://github.com/fulcrumgenomics/fgbio/wiki/Read-Structures
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.yml}"
+  - umibam:
+      type: file
+      description: Converted, unsorted BAM file with RX tag reporting UMI sequence (if any)
+      pattern: "*.{bam}"
+
+authors:
+  - "@lescai"

tests/config/pytest_modules.yml

@@ -378,6 +378,10 @@ fgbio/callmolecularconsensusreads:
   - modules/fgbio/callmolecularconsensusreads/**
   - tests/modules/fgbio/callmolecularconsensusreads/**
 
+fgbio/fastqtobam:
+  - modules/fgbio/fastqtobam/**
+  - tests/modules/fgbio/fastqtobam/**
+
 fgbio/sortbam:
   - modules/fgbio/sortbam/**
   - tests/modules/fgbio/sortbam/**

tests/modules/fgbio/fastqtobam/main.nf

@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+params.read_structure = "+T 12M11S+T"
+
+include { FGBIO_FASTQTOBAM } from '../../../../modules/fgbio/fastqtobam/main.nf' addParams( options: [:] )
+
+workflow test_fgbio_fastqtobam {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true), 
+                file(params.test_data['homo_sapiens']['illumina']['test_umi_2_fastq_gz'], checkIfExists: true) ] 
+              ]
+
+    FGBIO_FASTQTOBAM ( input, "${params.read_structure}" )
+}

tests/modules/fgbio/fastqtobam/test.yml

@@ -0,0 +1,10 @@
+- name: fgbio fastqtobam test_fgbio_fastqtobam
+  command: nextflow run tests/modules/fgbio/fastqtobam -entry test_fgbio_fastqtobam -c tests/config/nextflow.config
+  tags:
+    - fgbio/fastqtobam
+    - fgbio
+  files:
+    - path: output/fgbio/test_umi_converted.bam
+      md5sum: 9510735554e5eff29244077a72075fb6
+    - path: output/fgbio/versions.yml
+      md5sum: 524815093b96759060d0d800fc6a3f25