Merge pull request #1012 from KevinMenden/fix-clean-parameters

make cleanParameters more robust
nf-core · Apr 14, 2021 · cae6b1b · cae6b1b
2 parents fd24d08 + 50cbd38
commit cae6b1b
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,6 +19,7 @@
 * Added a timestamp to the trace + timetime + report + dag filenames to fix overwrite issue on AWS
 * Rewrite the `params_summary_log()` function to properly ignore unset params and have nicer formatting [[#971](https://github.com/nf-core/tools/issues/971)]
 * Fix overly strict `--max_time` formatting regex in template schema [[#973](https://github.com/nf-core/tools/issues/973)]
+* Convert `d` to `day` in the `cleanParameters` function to make Duration objects like `2d` pass the validation [[#858](https://github.com/nf-core/tools/issues/858)]
 
 ## [v1.13.3 - Copper Crocodile Resurrection :crocodile:](https://github.com/nf-core/tools/releases/tag/1.13.2) - [2021-03-24]
 

diff --git a/nf_core/pipeline-template/lib/NfcoreSchema.groovy b/nf_core/pipeline-template/lib/NfcoreSchema.groovy
@@ -243,7 +243,7 @@ class NfcoreSchema {
             }
             // Cast Duration to String
             if (p['value'].getClass() == nextflow.util.Duration) {
-                new_params.replace(p.key, p['value'].toString())
+                new_params.replace(p.key, p['value'].toString().replaceFirst(/d(?!\S)/, "day"))
             }
             // Cast LinkedHashMap to String
             if (p['value'].getClass() == LinkedHashMap) {