Merge pull request #719 from IdoBar/patch-6

Fix `mapdamage_rescaling` naming of output bam files

Author: jfy133

CHANGELOG.md

@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Fixed`
 
+- [#719](https://github.com/nf-core/eager/pull/719) - Fix filename for bam output of `mapdamage_rescaling`
 - [#707](https://github.com/nf-core/eager/pull/707) - Fix typo in UnifiedGenotyper IndelRealigner command
 - Fixed some Java tools not following process memory specifications
 - Updated template to nf-core/tools 1.13.2

main.nf

@@ -2009,8 +2009,8 @@ process mapdamage_rescaling {
     def singlestranded = strandedness == "single" ? '--single-stranded' : ''
     def size = params.large_ref ? '-c' : ''
     """
-    mapDamage -i ${bam} -r ${fasta} --rescale --rescale-out ${bam}_rescaled.bam --rescale-length-5p ${params.rescale_length_5p} --rescale-length-3p=${params.rescale_length_3p} ${singlestranded}
-    samtools index ${bam}_rescaled.bam ${size}
+    mapDamage -i ${bam} -r ${fasta} --rescale --rescale-out ${base}_rescaled.bam --rescale-length-5p ${params.rescale_length_5p} --rescale-length-3p=${params.rescale_length_3p} ${singlestranded}
+    samtools index ${base}_rescaled.bam ${size}
     """
 
 }