diff --git a/subworkflows/local/shortread_preprocessing.nf b/subworkflows/local/shortread_preprocessing.nf index 6e14423..d381d34 100644 --- a/subworkflows/local/shortread_preprocessing.nf +++ b/subworkflows/local/shortread_preprocessing.nf @@ -22,7 +22,7 @@ workflow SHORTREAD_PREPROCESSING { ch_versions = ch_versions.mix( SHORTREAD_FASTP.out.versions ) ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_FASTP.out.mqc ) } else if ( params.shortread_qc_tool == "adapterremoval" ) { - ch_processed_reads = SHORTREAD_ADAPTERREMOVAL ( reads ).reads + ch_processed_reads = SHORTREAD_ADAPTERREMOVAL ( reads, adapterlist ).reads ch_versions = ch_versions.mix( SHORTREAD_ADAPTERREMOVAL.out.versions ) ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_ADAPTERREMOVAL.out.mqc ) } else {