add Amps (#768)

* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Start work, continue once on non-mobile internet

* finished and working on conda

* Update modules/amps/main.nf

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

* Apply suggestions from code review

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

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

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+    // Do not publish versions.yml unless running from pytest workflow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

@@ -0,0 +1,47 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process AMPS {
+    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:[:], 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 maltextract_results
+    path taxon_list
+    val filter
+
+    output:
+    path "results/heatmap_overview_Wevid.json" , emit: json
+    path "results/heatmap_overview_Wevid.pdf"  , emit: summary_pdf
+    path "results/heatmap_overview_Wevid.tsv"  , emit: tsv
+    path "results/pdf_candidate_profiles/"     , emit: candidate_pdfs
+    path "versions.yml"                        , emit: version
+
+    script:
+    """
+    postprocessing.AMPS.r \\
+        -r $maltextract_results \\
+        -n $taxon_list \\
+        -m $filter \\
+        -t $task.cpus \\
+        -j \\
+        $options.args
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        amps: \$(echo \$(hops --version 2>&1) | sed 's/HOPS version//')
+    END_VERSIONS
+    """
+}

modules/amps/meta.yml

@@ -0,0 +1,66 @@
+name: amps
+description: Post-processing script of the MaltExtract component of the HOPS package
+keywords:
+  - malt
+  - MaltExtract
+  - HOPS
+  - amps
+  - alignment
+  - metagenomics
+  - ancient DNA
+  - aDNA
+  - palaeogenomics
+  - archaeogenomics
+  - microbiome
+  - authentication
+  - damage
+  - edit distance
+  - post Post-processing
+  - visualisation
+tools:
+  - amps:
+      description: Post-processing script of the MaltExtract tool for ancient metagenomics
+      homepage: "https://github.com/rhuebler/HOPS"
+      documentation: "https://github.com/keyfm/amps"
+      tool_dev_url: "https://github.com/keyfm/amps"
+      doi: "10.1186/s13059-019-1903-0"
+      licence: ['GPL >=3']
+
+input:
+  - maltextract_results:
+      type: directory
+      description: MaltExtract output directory
+      pattern: "results/"
+  - taxon_list:
+      type: file
+      description: List of target taxa to evaluate used in MaltExtract
+      pattern: "*.txt"
+  - filter:
+      type: string
+      description: The filter mode used in MaltExtract
+      pattern: "def_anc|default|scan|ancient|crawl"
+
+output:
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "versions.yml"
+  - json:
+      type: file
+      description: Candidate summary heatmap in MultiQC compatible JSON format
+      pattern: "heatmap_overview_Wevid.json"
+  - summary_pdf:
+      type: file
+      description: Candidate summary heatmap in PDF format
+      pattern: "heatmap_overview_Wevid.pdf"
+  - tsv:
+      type: file
+      description: Candidate summary heatmap in TSV format
+      pattern: "heatmap_overview_Wevid.tsv"
+  - candidate_pdfs:
+      type: directory
+      description: Directory of per sample output PDFs organised by reference
+      pattern: "pdf_candidate_profiles/"
+
+authors:
+  - "@jfy133"

tests/config/pytest_modules.yml

@@ -14,6 +14,10 @@ allelecounter:
   - modules/allelecounter/**
   - tests/modules/allelecounter/**
 
+amps:
+  - modules/amps/**
+  - tests/modules/amps/**
+
 arriba:
   - modules/arriba/**
   - tests/modules/arriba/**

tests/modules/amps/main.nf

@@ -0,0 +1,32 @@
+#!/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: [args: "-f def_anc"] )
+include { AMPS        } from '../../../modules/amps/main.nf' addParams( options: [:] )
+
+
+workflow test_amps {
+
+    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)
+    filter = "def_anc"
+
+    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)
+
+    AMPS ( MALTEXTRACT.out.results, taxon_list, filter )
+}

tests/modules/amps/test.yml

@@ -0,0 +1,11 @@
+- name: amps
+  command: nextflow run ./tests/modules/amps -entry test_amps -c tests/config/nextflow.config
+  tags:
+    - amps
+  files:
+    - path: output/amps/results/heatmap_overview_Wevid.json
+      md5sum: 82f484d02a9e3d0cc3d5bcdcc2965e44
+    - path: output/amps/results/heatmap_overview_Wevid.pdf
+    - path: output/amps/results/heatmap_overview_Wevid.tsv
+      md5sum: 1a7d565a37ef4d6054f7ade63fbadc2f
+    - path: output/amps/results/pdf_candidate_profiles/Severe_acute_respiratory_syndrome_coronavirus_2/stp1_test_1.rma6_Severe_acute_respiratory_syndrome_coronavirus_2_summary.pdf