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Fix: Missing import statements on error messages(#1566) #1712

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Oct 30, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -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

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4 changes: 2 additions & 2 deletions subworkflows/local/utils_nfcore_sarek_pipeline/main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand All @@ -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
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