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Install krakenuniq module
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118
modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf
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118
modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf
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process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::krakenuniq=1.0.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/krakenuniq:1.0.0--pl5321h19e8d03_0':
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'quay.io/biocontainers/krakenuniq:1.0.0--pl5321h19e8d03_0' }"
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input:
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tuple val(meta), path(fastqs)
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path db
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val ram_chunk_size
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val save_output_fastqs
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val report_file
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val save_output
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output:
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tuple val(meta), path('*.classified{.,_}*') , optional:true, emit: classified_reads_fastq
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tuple val(meta), path('*.unclassified{.,_}*') , optional:true, emit: unclassified_reads_fastq
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tuple val(meta), path('*classified.txt') , optional:true, emit: classified_assignment
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tuple val(meta), path('*report.txt') , emit: report
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def args2 = task.ext.args ?: ''
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def paired = meta.single_end ? "" : "--paired"
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def classified = meta.single_end ? '"\$PREFIX".classified.fastq' : '"\$PREFIX".classified#.fastq'
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def unclassified = meta.single_end ? '"\$PREFIX".unclassified.fastq' : '"\$PREFIX".unclassified#.fastq'
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def classified_option = save_output_fastqs ? "--classified-out ${classified}" : ""
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def unclassified_option = save_output_fastqs ? "--unclassified-out ${unclassified}" : ""
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def output_option = save_output ? '--output "\$PREFIX".krakenuniq.classified.txt' : ""
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def report = report_file ? '--report-file "\$PREFIX".krakenuniq.report.txt' : ""
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def compress_reads_command = save_output_fastqs ? "gzip --no-name *.fastq" : ""
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"""
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krakenuniq \\
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$args \\
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--db $db \\
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--preload $ram_chunk_size \\
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--threads $task.cpus
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for fastq in ${fastqs.join(' ')}; do \\
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PREFIX=\$(echo \$fastq)
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krakenuniq \\
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--db $db \\
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--threads $task.cpus \\
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$report \\
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$output_option \\
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$unclassified_option \\
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$classified_option \\
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$output_option \\
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$paired \\
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$args2 \\
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\$fastq
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done
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$compress_reads_command
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//')
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END_VERSIONS
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"""
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stub:
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def args = task.ext.args ?: ''
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def args2 = task.ext.args ?: ''
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def paired = meta.single_end ? "" : "--paired"
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def classified = meta.single_end ? '"\$PREFIX".classified.fastq' : '"\$PREFIX".classified#.fastq'
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def unclassified = meta.single_end ? '"\$PREFIX".unclassified.fastq' : '"\$PREFIX".unclassified#.fastq'
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def classified_option = save_output_fastqs ? "--classified-out ${classified}" : ""
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def unclassified_option = save_output_fastqs ? "--unclassified-out ${unclassified}" : ""
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def output_option = save_output ? '--output "\$PREFIX".krakenuniq.classified.txt' : ""
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def report = report_file ? '--report-file "\$PREFIX".krakenuniq.report.txt' : ""
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def compress_reads_command = save_output_fastqs ? "echo 'gzip --no-name *.fastq'" : ""
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"""
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echo "krakenuniq \\
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$args \\
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--db $db \\
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--preload $ram_chunk_size \\
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--threads $task.cpus"
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for fastq in ${fastqs.join(' ')}; do \\
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PREFIX=\$(echo \$fastq)
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echo "krakenuniq \\
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--db $db \\
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--threads $task.cpus \\
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$report \\
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$output_option \\
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$unclassified_option \\
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$classified_option \\
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$output_option \\
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$paired \\
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$args2 \\
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\$fastq"
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touch "\$PREFIX".classified.fastq.gz
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touch "\$PREFIX".krakenuniq.classified.txt
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touch "\$PREFIX".krakenuniq.report.txt
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touch "\$PREFIX".unclassified.fastq.gz
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done
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$compress_reads_command
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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77
modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml
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modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml
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name: "krakenuniq_preloadedkrakenuniq"
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description: Classifies metagenomic sequence data using unique k-mer counts
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keywords:
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- classify
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- metagenomics
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- kmers
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- fastq
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- db
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tools:
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- "krakenuniq":
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description: "Metagenomics classifier with unique k-mer counting for more specific results"
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homepage: https://github.com/fbreitwieser/krakenuniq
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documentation: https://github.com/fbreitwieser/krakenuniq
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doi: 10.1186/s13059-018-1568-0
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licence: ["MIT"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- fastqs:
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type: file
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description: List of input FastQ files
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- db:
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type: directory
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description: KrakenUniq database
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- ram_chunk_size:
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type: val
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description: Amount of maximum amount of RAM each chunk of database that should be loaded at any one time
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pattern: "*GB"
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- save_output_fastqs:
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type: boolean
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description: |
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If true, optional commands are added to save classified and unclassified reads
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as fastq files
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- save_reads_assignment:
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type: boolean
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description: |
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If true, an optional command is added to save a file reporting the taxonomic
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classification of each input read
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- classified_reads_fastq:
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type: file
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description: |
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Reads classified as belonging to any of the taxa
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on the KrakenUniq database.
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pattern: "*{fastq.gz}"
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- unclassified_reads_fastq:
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type: file
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description: |
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Reads not classified to any of the taxa
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on the KrakenUniq database.
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pattern: "*{fastq.gz}"
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- classified_assignment:
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type: file
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description: |
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KrakenUniq output file indicating the taxonomic assignment of
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each input read ## DOUBLE CHECK!!
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- report:
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type: file
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description: |
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KrakenUniq report containing stats about classified
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and not classifed reads.
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pattern: "*.{report.txt}"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@mjamy"
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