Merge pull request #619 from maxulysse/dev_AWS_megatests

fix issue with AWS megatests

Author: apeltzer

CHANGELOG.md

@@ -110,6 +110,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#602](https://github.com/nf-core/sarek/pull/602) - Fixed bug in `alignment_to_fastq` and added tests
 - [#609](https://github.com/nf-core/sarek/pull/609) - Remove unused intervals code, reorganize combined intervals file
 - [#615](https://github.com/nf-core/sarek/pull/615) - Fix ASCAT igenomes file paths
+- [#619](https://github.com/nf-core/sarek/pull/619) - Fix issue with checking samplesheet content with AWS
 
 ### Deprecated
 

workflows/sarek.nf

@@ -985,7 +985,7 @@ workflow.onComplete {
 def extract_csv(csv_file) {
 
     // check that the sample sheet is not 1 line or less, because it'll skip all subsequent checks if so.
-    new File(csv_file.toString()).withReader('UTF-8') { reader ->
+    file(csv_file).withReader('UTF-8') { reader ->
         def line, numberOfLinesInSampleSheet = 0;
         while ((line = reader.readLine()) != null) {numberOfLinesInSampleSheet++}
         if (numberOfLinesInSampleSheet < 2) {