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Merge pull request #285 from nf-core/update-kraken

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BUmp Kraken2 nf-core module to prevent huge logs
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James A. Fellows Yates 2023-04-21 05:57:27 +02:00 committed by GitHub
commit 003862d9ea
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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": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "7c695e0147df1157413e06246d9b0094617d3e6b",
"installed_by": ["modules"]
},
"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 classified_option = save_output_fastqs ? "--classified-out ${classified}" : ""
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" : ""
"""