diff --git a/conf/modules.config b/conf/modules.config index 62e7949d..8e913744 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -47,7 +47,7 @@ process { tag = { "${meta.id}_run${meta.run}" } } - withName: TRIMMOMATIC { + withName: TRIMMOMATIC { ext.args = "LEADING:30 TRAILING:30 SLIDINGWINDOW:4:20 MINLEN:35" publishDir = [ [ diff --git a/subworkflows/local/shortread_preprocessing.nf b/subworkflows/local/shortread_preprocessing.nf index f3822e1c..b71c47c2 100644 --- a/subworkflows/local/shortread_preprocessing.nf +++ b/subworkflows/local/shortread_preprocessing.nf @@ -65,7 +65,7 @@ workflow SHORTREAD_PREPROCESSING { ch_multiqc_files = ch_multiqc_files.mix(ADAPTERREMOVAL_PE.out.settings) ch_multiqc_files = ch_multiqc_files.mix(ADAPTERREMOVAL_SE.out.settings) } - else if (params.clip_tool == 'trimmomatic') { + else if (params.clip_tool == 'trimmomatic') { TRIMMOMATIC(ch_raw_short_reads)