Merge pull request #157 from apeltzer/publish_dedup

Adding in publishing dedup log files as well

Author: apeltzer

CHANGELOG.md

@@ -8,7 +8,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Added`
 
-* Clarified `--complexity_filter` flag to be specifically for poly G trimming.
+* [#152](https://github.com/nf-core/eager/pull/152) - Clarified `--complexity_filter` flag to be specifically for poly G trimming.
+* [#155](https://github.com/nf-core/eager/pull/155) - Added [Dedup log to output folders](https://github.com/nf-core/eager/issues/154)
 
 ### `Fixed`
 

main.nf

@@ -828,7 +828,9 @@ Step 6: DeDup / MarkDuplicates
 
 process dedup{
     tag "${bam.baseName}"
-    publishDir "${params.outdir}/deduplication/dedup"
+    publishDir "${params.outdir}/deduplication/dedup", mode: 'copy',
+        saveAs: {filename -> (filename.endsWith(".hist") || filename.endsWith(".log")) ? "${prefix}/$filename" : "$filename"}
+
 
     when:
     !params.skip_deduplication && params.dedupper == 'dedup'