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@ -31,7 +31,7 @@ process KRAKEN2_KRAKEN2 {
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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 readclassification_option = save_reads_assignment ? "--output ${prefix}.kraken2.classifiedreads.txt" : ""
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def readclassification_option = save_reads_assignment ? "--output ${prefix}.kraken2.classifiedreads.txt" : "--output /dev/null"
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def compress_reads_command = save_output_fastqs ? "pigz -p $task.cpus *.fastq" : ""
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"""
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