Merge pull request #1712 from pharmlovex/dev

Fix: Missing import statements on error messages(#1566)
nf-core · Oct 30, 2024 · 8ea4af9 · 8ea4af9
2 parents 1ba8cee + 4087d63
commit 8ea4af9
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diff --git 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
@@ -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