add: MALTEXTRACT (#725)

* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Start maltextract module

* start tests

* Get tests working now we have test data

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Changes after review

* Update tests/modules/maltextract/main.nf

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Update tests/modules/maltextract/main.nf

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Update tests/modules/maltextract/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

modules/maltextract/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/maltextract/main.nf

@@ -0,0 +1,44 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process MALTEXTRACT {
+
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
+
+    conda (params.enable_conda ? "bioconda::hops=0.35" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1"
+    } else {
+        container "quay.io/biocontainers/hops:0.35--hdfd78af_1"
+    }
+
+    input:
+    path rma6
+    path taxon_list
+    path ncbi_dir
+
+    output:
+    path "results"      , emit: results
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    """
+    MaltExtract \\
+        -Xmx${task.memory.toGiga()}g \\
+        -p $task.cpus \\
+        -i ${rma6.join(' ')} \\
+        -t $taxon_list \\
+        -r $ncbi_dir \\
+        -o results/ \\
+        $options.args
+
+    echo \$(MaltExtract --help | head -n 2 | tail -n 1) | sed 's/MaltExtract version//' > ${software}.version.txt
+    """
+}

modules/maltextract/meta.yml

@@ -0,0 +1,51 @@
+name: maltextract
+description: Tool for evaluation of MALT results for true positives of ancient metagenomic taxonomic screening
+keywords:
+  - malt
+  - MaltExtract
+  - HOPS
+  - alignment
+  - metagenomics
+  - ancient DNA
+  - aDNA
+  - palaeogenomics
+  - archaeogenomics
+  - microbiome
+  - authentication
+  - damage
+  - edit distance
+tools:
+  - maltextract:
+      description: Java tool to work with ancient metagenomics
+      homepage: https://github.com/rhuebler/hops
+      documentation: https://github.com/rhuebler/hops
+      tool_dev_url: https://github.com/rhuebler/hops
+      doi: "https://doi.org/10.1186/s13059-019-1903-0"
+      licence: ['GPL 3']
+
+input:
+  - rma6:
+      type: file
+      description: RMA6 files from MALT
+      pattern: "*.rma6"
+  - taxon_list:
+      type: file
+      description: List of target taxa to evaluate
+      pattern: "*.txt"
+  - ncbi_dir:
+      type: directory
+      description: Directory containing NCBI taxonomy map and tre files
+      pattern: "${ncbi_dir}/"
+
+output:
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - results:
+      type: directory
+      description: Directory containing MaltExtract text results files
+      pattern: "*.rma6"
+
+authors:
+  - "@jfy133"

tests/config/pytest_modules.yml

@@ -562,6 +562,10 @@ malt/run:
   - modules/malt/run/**
   - tests/modules/malt/run/**
 
+maltextract:
+  - modules/maltextract/**
+  - tests/modules/maltextract/**
+
 mash/sketch:
   - modules/mash/sketch/**
   - tests/modules/mash/sketch/**

tests/config/test_data.config

@@ -7,7 +7,6 @@ params {
             'genome' {
                 genome_fasta                                   = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta"
                 genome_fasta_fai                               = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta.fai"
-                genome_fasta_zip                               = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta.zip"
                 genome_dict                                    = "${test_data_dir}/genomics/sarscov2/genome/genome.dict"
                 genome_gff3                                    = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3"
                 genome_gff3_gz                                 = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3.gz"
@@ -25,6 +24,9 @@ params {
                 kraken2                                        = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2"
                 kraken2_tar_gz                                 = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2.tar.gz"
 
+                ncbi_taxmap_zip                                = "${test_data_dir}/genomics/sarscov2/genome/db/maltextract/ncbi_taxmap.zip"
+                taxon_list_txt                                 = "${test_data_dir}/genomics/sarscov2/genome/db/maltextract/taxon_list.txt"
+
                 all_sites_fas                                  = "${test_data_dir}/genomics/sarscov2/genome/alignment/all_sites.fas"
                 informative_sites_fas                          = "${test_data_dir}/genomics/sarscov2/genome/alignment/informative_sites.fas"
 

tests/modules/maltextract/main.nf

@@ -0,0 +1,27 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNZIP as UNZIP_MALT        } from '../../../modules/unzip/main.nf' addParams( options: [:] )
+include { UNZIP as UNZIP_MALTEXTRACT }  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: [:] )
+include { MALTEXTRACT } from '../../../modules/maltextract/main.nf' addParams( options: [:] )
+
+workflow test_maltextract {
+
+    fastas = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    gff = []
+    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"
+    taxon_list = file(params.test_data['sarscov2']['genome']['taxon_list_txt'], checkIfExists: true)
+    ncbi_dir = file(params.test_data['sarscov2']['genome']['ncbi_taxmap_zip'], checkIfExists: true)
+
+    UNZIP_MALT ( map_db )
+    UNZIP_MALTEXTRACT ( ncbi_dir )
+    MALT_BUILD ( fastas, seq_type, gff, UNZIP_MALT.out.unzipped_archive )
+    MALT_RUN ( input, mode, MALT_BUILD.out.index )
+    MALTEXTRACT ( MALT_RUN.out.rma6, taxon_list, UNZIP_MALTEXTRACT.out.unzipped_archive)
+}

tests/modules/maltextract/test.yml

@@ -0,0 +1,11 @@
+- name: maltextract
+  command: nextflow run ./tests/modules/maltextract -entry test_maltextract -c tests/config/nextflow.config
+  tags:
+    - maltextract
+  files:
+    - path: output/maltextract/results/error.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/maltextract/results/error.txt
+    - path: output/maltextract/results/log.txt
+      contains:
+        - "INFO: Peak memory"