mirror of
https://github.com/MillironX/taxprofiler.git
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119 lines
4.3 KiB
Text
119 lines
4.3 KiB
Text
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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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