Mercurial > repos > kkonganti > cfsan_centriflaken

comparison 0.2.1/modules/kraken2/classify/main.nf @ 47:30191f39a957

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"planemo upload"
author kkonganti
date Mon, 11 Jul 2022 12:19:48 -0400
parents 77494b0fa3c7
children
comparison
equal deleted inserted replaced
46:0dd0ebe5cddf 47:30191f39a957
26 def db = meta.kraken2_db ?: '' 26 def db = meta.kraken2_db ?: ''
27 def prefix = task.ext.prefix ?: "${meta.id}" 27 def prefix = task.ext.prefix ?: "${meta.id}"
28 def readList = reads.collect{ it.toString() } 28 def readList = reads.collect{ it.toString() }
29 def is_single_end = (meta.single_end || meta.is_assembly) ? true : false 29 def is_single_end = (meta.single_end || meta.is_assembly) ? true : false
30 def paired = is_single_end ? "" : "--paired" 30 def paired = is_single_end ? "" : "--paired"
31 def classified = is_single_end ? "${prefix}.classified.fastq" : "${prefix}.classified#.fastq" 31 def classified = is_single_end ? "--classified-out ${prefix}.classified.fastq" : "--classified-out ${prefix}.classified#.fastq"
32 def unclassified = is_single_end ? "${prefix}.unclassified.fastq" : "${prefix}.unclassified#.fastq" 32 def unclassified = is_single_end ? "--unclassified-out ${prefix}.unclassified.fastq" : "--unclassified-out ${prefix}.unclassified#.fastq"
33 args += (reads.getName().endsWith(".gz") ? ' --gzip-compressed ' : '') 33 args += (reads.getName().endsWith(".gz") ? ' --gzip-compressed ' : '')
34 """ 34 """
35 kraken2 \\ 35 kraken2 \\
36 --db $db \\ 36 --db $db \\
37 --threads $task.cpus \\ 37 --threads $task.cpus \\
38 --unclassified-out $unclassified \\ 38 $unclassified \\
39 --classified-out $classified \\ 39 $classified \\
40 --report ${prefix}.kraken2.report.txt \\ 40 --report ${prefix}.kraken2.report.txt \\
41 --output ${prefix}.kraken2.output.txt \\ 41 --output ${prefix}.kraken2.output.txt \\
42 $paired \\ 42 $paired \\
43 $args \\ 43 $args \\
44 $reads 44 $reads