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BUmp Kraken2 nf-core module to prevent huge logs

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This commit is contained in:
James Fellows Yates 2023-04-20 15:20:26 +02:00
parent 255b492b44
commit 0ed110c529
2 changed files with 2 additions and 2 deletions
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2
modules.json
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@ -103,7 +103,7 @@
}, },
"kraken2/kraken2": { "kraken2/kraken2": {
"branch": "master", "branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "git_sha": "7c695e0147df1157413e06246d9b0094617d3e6b",
"installed_by": ["modules"] "installed_by": ["modules"]
}, },
"krakentools/combinekreports": { "krakentools/combinekreports": {

2
modules/nf-core/kraken2/kraken2/main.nf generated
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@ -31,7 +31,7 @@ process KRAKEN2_KRAKEN2 {
def unclassified = meta.single_end ? "${prefix}.unclassified.fastq" : "${prefix}.unclassified#.fastq" def unclassified = meta.single_end ? "${prefix}.unclassified.fastq" : "${prefix}.unclassified#.fastq"
def classified_option = save_output_fastqs ? "--classified-out ${classified}" : "" def classified_option = save_output_fastqs ? "--classified-out ${classified}" : ""
def unclassified_option = save_output_fastqs ? "--unclassified-out ${unclassified}" : "" def unclassified_option = save_output_fastqs ? "--unclassified-out ${unclassified}" : ""
def readclassification_option = save_reads_assignment ? "--output ${prefix}.kraken2.classifiedreads.txt" : "" def readclassification_option = save_reads_assignment ? "--output ${prefix}.kraken2.classifiedreads.txt" : "--output /dev/null"
def compress_reads_command = save_output_fastqs ? "pigz -p $task.cpus *.fastq" : "" def compress_reads_command = save_output_fastqs ? "pigz -p $task.cpus *.fastq" : ""
""" """