add module for tbprofiler (#947)

* add module for tbprofiler

* Update test.yml

* Update meta.yml

Co-authored-by: Abhinav Sharma <abhi18av@users.noreply.github.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

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+    // Do not publish versions.yml unless running from pytest workflow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

@@ -0,0 +1,48 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process TBPROFILER_PROFILE {
+    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), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::tb-profiler=3.0.8" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/tb-profiler:3.0.8--pypyh5e36f6f_0"
+    } else {
+        container "quay.io/biocontainers/tb-profiler:3.0.8--pypyh5e36f6f_0"
+    }
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path("bam/*.bam")     , emit: bam
+    tuple val(meta), path("results/*.csv") , emit: csv, optional: true
+    tuple val(meta), path("results/*.json"), emit: json
+    tuple val(meta), path("results/*.txt") , emit: txt, optional: true
+    tuple val(meta), path("vcf/*.vcf.gz")  , emit: vcf
+    path "versions.yml"                    , emit: versions
+
+    script:
+    prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def input_reads = meta.single_end ? "--read1 $reads" : "--read1 ${reads[0]} --read2 ${reads[1]}"
+    """
+    tb-profiler \\
+        profile \\
+        $options.args \\
+        --prefix ${prefix} \\
+        --threads $task.cpus \\
+        $input_reads
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}:  \$( echo \$(tb-profiler --version 2>&1) | sed 's/TBProfiler version //')
+    END_VERSIONS
+    """
+}

modules/tbprofiler/profile/meta.yml

@@ -0,0 +1,59 @@
+name: tbprofiler_profile
+description: A tool to detect resistance and lineages of M. tuberculosis genomes
+keywords:
+  - Mycobacterium tuberculosis
+  - resistance
+  - serotype
+tools:
+  - tbprofiler:
+      description: Profiling tool for Mycobacterium tuberculosis to detect drug resistance and lineage from WGS data
+      homepage: https://github.com/jodyphelan/TBProfiler
+      documentation: https://jodyphelan.gitbook.io/tb-profiler/
+      tool_dev_url: https://github.com/jodyphelan/TBProfiler
+      doi: "10.1186/s13073-019-0650-x"
+      licence: ['GPL v3']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: FASTQ file
+      pattern: "*.{fastq.gz,fq.gz}"
+
+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"
+  - bam:
+      type: file
+      description: BAM file with alignment details
+      pattern: "*.bam"
+  - csv:
+      type: file
+      description: Optional CSV formated result file of resistance and strain type
+      pattern: "*.csv"
+  - json:
+      type: file
+      description: JSON formated result file of resistance and strain type
+      pattern: "*.json"
+  - txt:
+      type: file
+      description: Optional text file of resistance and strain type
+      pattern: "*.txt"
+  - vcf:
+      type: file
+      description: VCF with variant info again refernce genomes
+      pattern: "*.vcf"
+
+authors:
+  - "@rpetit3"

tests/config/pytest_modules.yml

@@ -1251,6 +1251,10 @@ tabix/tabix:
   - modules/tabix/tabix/**
   - tests/modules/tabix/tabix/**
 
+tbprofiler/profile:
+  - modules/tbprofiler/profile/**
+  - tests/modules/tbprofiler/profile/**
+
 tiddit/cov:
   - modules/tiddit/cov/**
   - tests/modules/tiddit/cov/**

tests/modules/tbprofiler/profile/main.nf

@@ -0,0 +1,24 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { TBPROFILER_PROFILE as TBPROFILER_PROFILE_ILLUMINA } from '../../../../modules/tbprofiler/profile/main.nf' addParams( options: [args: '--platform illumina'] )
+include { TBPROFILER_PROFILE as TBPROFILER_PROFILE_NANOPORE} from '../../../../modules/tbprofiler/profile/main.nf' addParams( options: [args: '--platform nanopore'] )
+
+workflow test_tbprofiler_profile_illumina {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] ]
+
+    TBPROFILER_PROFILE_ILLUMINA ( input )
+}
+
+
+workflow test_tbprofiler_profile_nanopore {
+    
+    input = [ [ id:'test', single_end:true ], // meta map
+              file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
+
+    TBPROFILER_PROFILE_NANOPORE ( input )
+}

tests/modules/tbprofiler/profile/test.yml

@@ -0,0 +1,21 @@
+- name: tbprofiler profile illumina
+  command: nextflow run ./tests/modules/tbprofiler/profile -entry test_tbprofiler_profile_illumina -c tests/config/nextflow.config
+  tags:
+    - tbprofiler
+    - tbprofiler/profile
+  files:
+    - path: output/tbprofiler/bam/test.bam
+    - path: output/tbprofiler/results/test.results.json
+      contains: ['genome_positions', 'locus_tag', 'tbprofiler_version']
+    - path: output/tbprofiler/vcf/test.targets.csq.vcf.gz
+
+- name: tbprofiler profile nanopore
+  command: nextflow run ./tests/modules/tbprofiler/profile -entry test_tbprofiler_profile_nanopore -c tests/config/nextflow.config
+  tags:
+    - tbprofiler
+    - tbprofiler/profile
+  files:
+    - path: output/tbprofiler/bam/test.bam
+    - path: output/tbprofiler/results/test.results.json
+      contains: ['genome_positions', 'locus_tag', 'tbprofiler_version']
+    - path: output/tbprofiler/vcf/test.targets.csq.vcf.gz