Merge pull request #821 from FriederikeHanssen/fix_input_finding

Use putIfAbsent
nf-core · Nov 10, 2022 · 8e5afb3 · 8e5afb3
2 parents 9337d11 + b8837cc
commit 8e5afb3
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#806](https://github.com/nf-core/sarek/pull/806) - Refactor all tests
 - [#806](https://github.com/nf-core/sarek/pull/806) - Split up `modules.config` file
 - [#810](https://github.com/nf-core/sarek/pull/810) - Update CHANGELOG
+- [#821](https://github.com/nf-core/sarek/pull/821) - Change `replace` to `putIfAbsent` for automatic search of `input` if none is provided to avoid overwriting values
 
 ### Fixed
 

diff --git a/lib/WorkflowSarek.groovy b/lib/WorkflowSarek.groovy
@@ -81,20 +81,20 @@ class WorkflowSarek {
                                             System.exit(1);
                                             break
             case 'markduplicates':          log.warn "Using file ${params.outdir}/csv/mapped.csv"
-                                            params.replace("input","${params.outdir}/csv/mapped.csv");
+                                            params.putIfAbsent("input","${params.outdir}/csv/mapped.csv");
                                             break
             case 'prepare_recalibration':   log.warn "Using file ${params.outdir}/csv/markduplicates_no_table.csv"
-                                            params.replace("input", "${params.outdir}/csv/markduplicates_no_table.csv");
+                                            params.putIfAbsent("input", "${params.outdir}/csv/markduplicates_no_table.csv");
                                             break
             case 'recalibrate':             log.warn "Using file ${params.outdir}/csv/markduplicates.csv"
-                                            params.replace("input", "${params.outdir}/csv/markduplicates.csv");
+                                            params.putIfAbsent("input", "${params.outdir}/csv/markduplicates.csv");
                                             break
             case 'variant_calling':         log.warn "Using file ${params.outdir}/csv/recalibrated.csv"
-                                            params.replace("input", "${params.outdir}/csv/recalibrated.csv");
+                                            params.putIfAbsent("input", "${params.outdir}/csv/recalibrated.csv");
                                             break
             // case 'controlfreec':         csv_file = file("${params.outdir}/variant_calling/csv/control-freec_mpileup.csv", checkIfExists: true); break
             case 'annotate':                log.warn "Using file ${params.outdir}/csv/variantcalled.csv"
-                                            params.replace("input","${params.outdir}/csv/variantcalled.csv");
+                                            params.putIfAbsent("input","${params.outdir}/csv/variantcalled.csv");
                                             break
             default:    log.warn "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'"
                         exit 1, "Unknown step $params.step"