diff --git a/subworkflows/local/utils_nfcore_eager_pipeline/main.nf b/subworkflows/local/utils_nfcore_eager_pipeline/main.nf index 2964373ba..d81dbddbb 100644 --- a/subworkflows/local/utils_nfcore_eager_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_eager_pipeline/main.nf @@ -233,7 +233,7 @@ def validateInputParameters() { !params.metagenomics_maltextract_ncbidir ) ){ exit 1, ("[nf-core/eager] ERROR: Metagenomics: You picked MALT with postprocessing but didnt provided required input files. Please provide the --metagenomics_maltextract_taxonlist and --metagenomics_maltextract_ncbidir flags") } - if ( params.run_metagenomics && params.preprocessing_skippairmerging ) { log.warn("[nf-core/eager] WARNING: --preprocessing_skippairmerging selected in combination for metagenomics! All singletons from paired end samples will be discarded prior to input for metagenomics screening! Additionally, this may be inappropriate for metaphlan, which does not utilize paired-end information!") } + if ( params.run_metagenomics && params.preprocessing_skippairmerging ) { log.warn("[nf-core/eager] WARNING: --preprocessing_skippairmerging selected in combination for metagenomics! All singletons from paired end samples will be discarded prior to input for metagenomics screening! This may be inappropriate for metaphlan, which does not utilize paired-end information!") } if ( params.run_metagenomics && params.preprocessing_skippairmerging && params.metagenomics_profiling_tool == 'malt' ) { exit 1, ("[nf-core/eager] ERROR: --preprocessing_skippairmerging selected in combination with MALT for metagenomics! MALT cannot accept separated read pair information, please remove --preprocessing_skippairmerging parameter.") } if ( params.run_genotyping && ! params.genotyping_tool ) { exit 1, ("[nf-core/eager] ERROR: --run_genotyping was specified, but no --genotyping_tool was specified.") } if ( params.run_genotyping && ! params.genotyping_source ) { exit 1, ("[nf-core/eager] ERROR: --run_genotyping was specified, but no --genotyping_source was specified.") }