Merge pull request #265 from nschcolnicov/fix_adapter

Fixed adapter removal

CHANGELOG.md

@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Fixed`
 
 - [#253](https://github.com/nf-core/demultiplex/pull/253) Fixed mkfastq output channels.
+- [#264](https://github.com/nf-core/demultiplex/pull/264) Fixed adapter removal for input samplesheets without lane information.
 
 ## 1.5.0 - 2024-08-12
 

workflows/demultiplex.nf

@@ -77,8 +77,8 @@ workflow DEMULTIPLEX {
                 [ "${item[0].id}${suffix}_no_adapters.csv", AdapterRemover.removeAdaptersFromSampleSheet(item[1]) ]
             }
             .map { file -> //build meta again from file name
-                def meta_id = (file =~ /([^\/]+)(?=\.(lane|_no_adapters))/)[0][1] //extracts everything from the last "/" until ".lane" or "_no_adapters"
-                def meta_lane = (file =~ /\.lane(\d+)/)[0][1].toInteger() //extracts number after ".lane" until next "_", must be int to match lane value from meta
+                def meta_id = (file =~ /.*\/(.*?)(\.lane|_no_adapters)/)[0][1] //extracts everything from the last "/" until ".lane" or "_no_adapters"
+                def meta_lane = (file.getName().contains('.lane')) ? (file =~ /\.lane(\d+)/)[0][1].toInteger() : null //extracts number after ".lane" until next "_", must be int to match lane value from meta
                 [[id: meta_id, lane: meta_lane],file]
             }
         ch_samplesheet_new = ch_samplesheet