module: MALT/RUN (#646)

* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Add MALT with incomplete tests

* Parameter typo fix

* Clean up test yaml

* Finish MALT module prior UNZIP and MALT_BUILD modiules

* Add required modules for tests

* Sync test out with malt-build

* Fix input parameters in tests based on final build module

* Update modules/malt/run/meta.yml

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>

modules/malt/run/functions.nf

@@ -0,0 +1,68 @@
+//
+//  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"
+        }
+    }
+}

modules/malt/run/main.nf

@@ -0,0 +1,54 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process MALT_RUN {
+
+    label 'process_high_memory'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
+
+    conda (params.enable_conda ? "bioconda::malt=0.5.2" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/malt:0.5.2--0"
+    } else {
+        container "quay.io/biocontainers/malt:0.5.2--0"
+    }
+
+    input:
+    path fastqs
+    val mode
+    path index
+
+    output:
+    path "*.rma6"                          , emit: rma6
+    path "*.{tab,text,sam}",  optional:true, emit: alignments
+    path "*.log"                           , emit: log
+    path "*.version.txt"                   , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def avail_mem = 6
+    if (!task.memory) {
+        log.info '[MALT_RUN] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+
+    """
+    malt-run \\
+        -J-Xmx${avail_mem}g \\
+        -t ${task.cpus} \\
+        -v \\
+        -o . \\
+        $options.args \\
+        --inFile ${fastqs.join(' ')} \\
+        -m $mode \\
+        --index $index/ |&tee malt-run.log
+
+    echo \$(malt-run --help  2>&1) | grep -o 'version.* ' | cut -f 1 -d ',' | cut -f2 -d ' ' > ${software}.version.txt
+    """
+}

modules/malt/run/meta.yml

@@ -0,0 +1,53 @@
+name: malt_run
+description: MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics.
+keywords:
+  - malt
+  - alignment
+  - metagenomics
+  - ancient DNA
+  - aDNA
+  - palaeogenomics
+  - archaeogenomics
+  - microbiome
+tools:
+  - malt:
+      description: A tool for mapping metagenomic data
+      homepage: https://www.wsi.uni-tuebingen.de/lehrstuehle/algorithms-in-bioinformatics/software/malt/
+      documentation: https://software-ab.informatik.uni-tuebingen.de/download/malt/manual.pdf
+      tool_dev_url: None
+      doi: "10.1038/s41559-017-0446-6"
+      licence: ['GPL v3']
+
+input:
+  - fastqs:
+      type: file
+      description: Input FASTQ files
+      pattern: "*.{fastq.gz,fq.gz}"
+  - mode:
+      type: string
+      description: Program mode
+      pattern: 'Unknown|BlastN|BlastP|BlastX|Classifier'
+  - index:
+      type: directory
+      description: Index/database directory from malt-build
+      pattern: '*/'
+output:
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - rma6:
+      type: file
+      description: MEGAN6 RMA6 file
+      pattern: "*.rma6"
+  - sam:
+      type: file
+      description: Alignment files in Tab, Text or MEGAN-compatible SAM format
+      pattern: "*.{tab,txt,sam}"
+  - log:
+      type: file
+      description: Log of verbose MALT stdout
+      pattern: "malt-run.log"
+
+authors:
+  - "@jfy133"

tests/config/pytest_modules.yml

@@ -478,6 +478,10 @@ malt/build:
   - modules/malt/build/**
   - tests/modules/malt/build_test/**
 
+malt/run:
+  - modules/malt/run/**
+  - tests/modules/malt/run/**
+
 mash/sketch:
   - modules/mash/sketch/**
   - tests/modules/mash/sketch/**

tests/modules/malt/run/main.nf

@@ -0,0 +1,21 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNZIP } from '../../../../modules/unzip/main.nf' addParams( options: [:] )
+include { MALT_BUILD } from  '../../../../modules/malt/build/main.nf' addParams( options: [:] )
+include { MALT_RUN } from '../../../../modules/malt/run/main.nf' addParams( options: [:] )
+
+workflow test_malt_run {
+
+    fastas = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    gff = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
+    seq_type = "DNA"
+    map_db = file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Jan2021.db.zip", checkIfExists: true)
+    input = file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    mode = "BlastN"
+
+    UNZIP ( map_db )
+    MALT_BUILD ( fastas, seq_type, gff, UNZIP.out.unzipped_archive )
+    MALT_RUN ( input, mode, MALT_BUILD.out.index )
+}

tests/modules/malt/run/test.yml

@@ -0,0 +1,11 @@
+## TODO nf-core: Please run the following command to build this file:
+#                nf-core modules create-test-yml malt/run
+- name: malt run
+  command: nextflow run ./tests/modules/malt/run -entry test_malt_run -c tests/config/nextflow.config
+  tags:
+    - malt
+    - malt/run
+  files:
+    - path: output/malt/test_1.rma6
+    - path: output/malt/malt-run.log
+