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Improves kraken2 output glob (#1987)

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* Improves kraken2 output glob

* Further strictness

* Further improvements
This commit is contained in:
James A. Fellows Yates 2022-08-31 15:42:44 +02:00 committed by GitHub
parent 9d489648a7
commit 409a308ba4
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1 changed files with 11 additions and 11 deletions
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18
modules/kraken2/kraken2/main.nf
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@ -14,9 +14,9 @@ process KRAKEN2_KRAKEN2 {
val save_reads_assignment val save_reads_assignment
output: output:
tuple val(meta), path('*classified*') , optional:true, emit: classified_reads_fastq 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('*.unclassified{.,_}*') , optional:true, emit: unclassified_reads_fastq
tuple val(meta), path('*classifiedreads*'), optional:true, emit: classified_reads_assignment tuple val(meta), path('*classifiedreads.txt') , optional:true, emit: classified_reads_assignment
tuple val(meta), path('*report.txt') , emit: report tuple val(meta), path('*report.txt') , emit: report
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
@ -29,9 +29,9 @@ process KRAKEN2_KRAKEN2 {
def paired = meta.single_end ? "" : "--paired" def paired = meta.single_end ? "" : "--paired"
def classified = meta.single_end ? "${prefix}.classified.fastq" : "${prefix}.classified#.fastq" def classified = meta.single_end ? "${prefix}.classified.fastq" : "${prefix}.classified#.fastq"
def unclassified = meta.single_end ? "${prefix}.unclassified.fastq" : "${prefix}.unclassified#.fastq" def unclassified = meta.single_end ? "${prefix}.unclassified.fastq" : "${prefix}.unclassified#.fastq"
def classified_command = save_output_fastqs ? "--classified-out ${classified}" : "" def classified_option = save_output_fastqs ? "--classified-out ${classified}" : ""
def unclassified_command = save_output_fastqs ? "--unclassified-out ${unclassified}" : "" def unclassified_option = save_output_fastqs ? "--unclassified-out ${unclassified}" : ""
def readclassification_command = save_reads_assignment ? "--output ${prefix}.kraken2.classifiedreads.txt" : "" def readclassification_option = save_reads_assignment ? "--output ${prefix}.kraken2.classifiedreads.txt" : ""
def compress_reads_command = save_output_fastqs ? "pigz -p $task.cpus *.fastq" : "" def compress_reads_command = save_output_fastqs ? "pigz -p $task.cpus *.fastq" : ""
""" """
@ -40,9 +40,9 @@ process KRAKEN2_KRAKEN2 {
--threads $task.cpus \\ --threads $task.cpus \\
--report ${prefix}.kraken2.report.txt \\ --report ${prefix}.kraken2.report.txt \\
--gzip-compressed \\ --gzip-compressed \\
$unclassified_command \\ $unclassified_option \\
$classified_command \\ $classified_option \\
$readclassification_command \\ $readclassification_option \\
$paired \\ $paired \\
$args \\ $args \\
$reads $reads