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BUmp Kraken2 nf-core module to prevent huge logs
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parent
255b492b44
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2 changed files with 2 additions and 2 deletions
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@ -103,7 +103,7 @@
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},
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},
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"kraken2/kraken2": {
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"kraken2/kraken2": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "7c695e0147df1157413e06246d9b0094617d3e6b",
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"installed_by": ["modules"]
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"installed_by": ["modules"]
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},
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},
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"krakentools/combinekreports": {
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"krakentools/combinekreports": {
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2
modules/nf-core/kraken2/kraken2/main.nf
generated
2
modules/nf-core/kraken2/kraken2/main.nf
generated
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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 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 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 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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def compress_reads_command = save_output_fastqs ? "pigz -p $task.cpus *.fastq" : ""
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"""
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"""
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