diff --git a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf index a897dfebe5..f4983278a1 100644 --- a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf @@ -349,7 +349,7 @@ def retrieveInput(need_input, step, outdir) { def input = null if (!params.input && !params.build_only_index) { switch (step) { - case 'mapping': Nextflow.error("Can't start with step $step without samplesheet") + case 'mapping': error("Can't start $step step without samplesheet") break case 'markduplicates': log.warn("Using file ${outdir}/csv/mapped.csv"); input = outdir + "/csv/mapped.csv" @@ -368,7 +368,7 @@ def retrieveInput(need_input, step, outdir) { input = outdir + "/csv/variantcalled.csv" break default: log.warn("Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'") - Nextflow.error("Unknown step $step") + error("Unknown step $step") } } return input