Merge pull request #190 from apeltzer/fix-dedup-bam

Fix dedup bam

Author: apeltzer

CHANGELOG.md

@@ -10,8 +10,10 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 * [#186](https://github.com/nf-core/eager/pull/186) - Make FastQC skipping [possible]
 /(https://github.com/nf-core/eager/issues/182)
+
 ### `Fixed`
 * [#172](https://github.com/nf-core/eager/pull/152) - DamageProfiler errors [won't crash entire pipeline anymore](https://github.com/nf-core/eager/issues/171)
+* [#174](https://github.com/nf-core/eager/pull/190) - Publish DeDup files [properly](https://github.com/nf-core/eager/issues/183) 
 
 ### `Dependencies`
 

main.nf

@@ -908,8 +908,7 @@ Step 6: DeDup / MarkDuplicates
 process dedup{
     tag "${bam.baseName}"
     publishDir "${params.outdir}/deduplication/dedup", mode: 'copy',
-        saveAs: {filename -> (filename.endsWith(".hist") || filename.endsWith(".log")) ? "${prefix}/$filename" : "$filename"}
-
+        saveAs: {filename -> "${prefix}/$filename"}
 
     when:
     !params.skip_deduplication && params.dedupper == 'dedup'