diff --git a/CHANGELOG.md b/CHANGELOG.md index 4a583aaf26..e14914386d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -37,6 +37,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [1694](https://github.com/nf-core/sarek/pull/1694) - Fix manifest DOI display on CLI - [1695](https://github.com/nf-core/sarek/pull/1695) - Fix and update input_schema.json - [1702](https://github.com/nf-core/sarek/pull/1702) - Update nf-schema tests that were not failing on lenient mode +- [1712](https://github.com/nf-core/sarek/pull/1712) - Fix missing import statements on error messages when starting without samplesheet ### Removed 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