Install krakenuniq module

modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf

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+process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
+    tag "$meta.id"
+    label 'process_high'
+
+    conda (params.enable_conda ? "bioconda::krakenuniq=1.0.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/krakenuniq:1.0.0--pl5321h19e8d03_0':
+        'quay.io/biocontainers/krakenuniq:1.0.0--pl5321h19e8d03_0' }"
+
+    input:
+    tuple val(meta), path(fastqs)
+    path  db
+    val ram_chunk_size
+    val save_output_fastqs
+    val report_file
+    val save_output
+
+    output:
+    tuple val(meta), path('*.classified{.,_}*')     , optional:true, emit: classified_reads_fastq
+    tuple val(meta), path('*.unclassified{.,_}*')   , optional:true, emit: unclassified_reads_fastq
+    tuple val(meta), path('*classified.txt')        , optional:true, emit: classified_assignment
+    tuple val(meta), path('*report.txt')                           , emit: report
+
+    path "versions.yml"                                            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args ?: ''
+
+    def paired       = meta.single_end ? "" : "--paired"
+    def classified   = meta.single_end ? '"\$PREFIX".classified.fastq'   : '"\$PREFIX".classified#.fastq'
+    def unclassified = meta.single_end ? '"\$PREFIX".unclassified.fastq' : '"\$PREFIX".unclassified#.fastq'
+    def classified_option = save_output_fastqs ? "--classified-out ${classified}" : ""
+    def unclassified_option = save_output_fastqs ? "--unclassified-out ${unclassified}" : ""
+    def output_option = save_output ? '--output "\$PREFIX".krakenuniq.classified.txt' : ""
+    def report = report_file ? '--report-file "\$PREFIX".krakenuniq.report.txt' : ""
+    def compress_reads_command = save_output_fastqs ? "gzip --no-name *.fastq" : ""
+
+    """
+    krakenuniq \\
+        $args \\
+        --db $db \\
+        --preload $ram_chunk_size \\
+        --threads $task.cpus
+
+    for fastq in ${fastqs.join(' ')}; do \\
+        PREFIX=\$(echo \$fastq)
+        krakenuniq \\
+            --db $db \\
+            --threads $task.cpus \\
+            $report \\
+            $output_option \\
+            $unclassified_option \\
+            $classified_option \\
+            $output_option \\
+            $paired \\
+            $args2 \\
+            \$fastq
+    done
+
+    $compress_reads_command
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args ?: ''
+
+    def paired       = meta.single_end ? "" : "--paired"
+    def classified   = meta.single_end ? '"\$PREFIX".classified.fastq'   : '"\$PREFIX".classified#.fastq'
+    def unclassified = meta.single_end ? '"\$PREFIX".unclassified.fastq' : '"\$PREFIX".unclassified#.fastq'
+    def classified_option = save_output_fastqs ? "--classified-out ${classified}" : ""
+    def unclassified_option = save_output_fastqs ? "--unclassified-out ${unclassified}" : ""
+    def output_option = save_output ? '--output "\$PREFIX".krakenuniq.classified.txt' : ""
+    def report = report_file ? '--report-file "\$PREFIX".krakenuniq.report.txt' : ""
+    def compress_reads_command = save_output_fastqs ? "echo 'gzip --no-name *.fastq'" : ""
+    """
+    echo "krakenuniq \\
+        $args \\
+        --db $db \\
+        --preload $ram_chunk_size \\
+        --threads $task.cpus"
+
+    for fastq in ${fastqs.join(' ')}; do \\
+        PREFIX=\$(echo \$fastq)
+        echo "krakenuniq \\
+            --db $db \\
+            --threads $task.cpus \\
+            $report \\
+            $output_option \\
+            $unclassified_option \\
+            $classified_option \\
+            $output_option \\
+            $paired \\
+            $args2 \\
+            \$fastq"
+
+        touch "\$PREFIX".classified.fastq.gz
+        touch "\$PREFIX".krakenuniq.classified.txt
+        touch "\$PREFIX".krakenuniq.report.txt
+        touch "\$PREFIX".unclassified.fastq.gz
+    done
+
+    $compress_reads_command
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//')
+    END_VERSIONS
+    """
+}

modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml

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+name: "krakenuniq_preloadedkrakenuniq"
+description: Classifies metagenomic sequence data using unique k-mer counts
+keywords:
+  - classify
+  - metagenomics
+  - kmers
+  - fastq
+  - db
+tools:
+  - "krakenuniq":
+      description: "Metagenomics classifier with unique k-mer counting for more specific results"
+      homepage: https://github.com/fbreitwieser/krakenuniq
+      documentation: https://github.com/fbreitwieser/krakenuniq
+      doi: 10.1186/s13059-018-1568-0
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fastqs:
+      type: file
+      description: List of input FastQ files
+  - db:
+      type: directory
+      description: KrakenUniq database
+  - ram_chunk_size:
+      type: val
+      description: Amount of maximum amount of RAM each chunk of database that should be loaded at any one time
+      pattern: "*GB"
+  - save_output_fastqs:
+      type: boolean
+      description: |
+        If true, optional commands are added to save classified and unclassified reads
+        as fastq files
+  - save_reads_assignment:
+      type: boolean
+      description: |
+        If true, an optional command is added to save a file reporting the taxonomic
+        classification of each input read
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - classified_reads_fastq:
+      type: file
+      description: |
+        Reads classified as belonging to any of the taxa
+        on the KrakenUniq database.
+      pattern: "*{fastq.gz}"
+  - unclassified_reads_fastq:
+      type: file
+      description: |
+        Reads not classified to any of the taxa
+        on the KrakenUniq database.
+      pattern: "*{fastq.gz}"
+  - classified_assignment:
+      type: file
+      description: |
+        KrakenUniq output file indicating the taxonomic assignment of
+        each input read ## DOUBLE CHECK!!
+  - report:
+      type: file
+      description: |
+        KrakenUniq report containing stats about classified
+        and not classifed reads.
+      pattern: "*.{report.txt}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@mjamy"