diff --git a/modules.json b/modules.json index 9aa617a..f69c777 100644 --- a/modules.json +++ b/modules.json @@ -103,7 +103,7 @@ }, "kraken2/kraken2": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "7c695e0147df1157413e06246d9b0094617d3e6b", "installed_by": ["modules"] }, "krakentools/combinekreports": { diff --git a/modules/nf-core/kraken2/kraken2/main.nf b/modules/nf-core/kraken2/kraken2/main.nf index 1b9e760..5901064 100644 --- a/modules/nf-core/kraken2/kraken2/main.nf +++ b/modules/nf-core/kraken2/kraken2/main.nf @@ -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" : "" """