Merge pull request #200 from apeltzer/dev

Minor fixes + additional tests

Author: apeltzer

CHANGELOG.md

@@ -18,8 +18,9 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 * [#176](https://github.com/nf-core/eager/pull/176) - Increase runtime for DamageProfiler on [large reference genomes](https://github.com/nf-core/eager/issues/173)
 * [#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)
-* [#196](https://github.com/nf-core/eager/pull/190) - Fix reference [issues](https://github.com/nf-core/eager/issues/150)
-* [#196](https://github.com/nf-core/eager/pull/190) - Fix issues with PE data being mapped incompletely
+* [#196](https://github.com/nf-core/eager/pull/196) - Fix reference [issues](https://github.com/nf-core/eager/issues/150)
+* [#196](https://github.com/nf-core/eager/pull/196) - Fix issues with PE data being mapped incompletely
+* [#200](https://github.com/nf-core/eager/pull/200) - Fix minor issue with some [typos](https://github.com/nf-core/eager/pull/196)
 
 ### `Dependencies`
 

main.nf

@@ -728,7 +728,7 @@ process bwa {
     """
     } else {
     //PE collapsed, or SE data 
-    prefix = "${reads}.baseName}"
+    prefix = "${reads.baseName}"
     """
     bwa aln -t ${task.cpus} $fasta $reads -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${prefix}.sai
     bwa samse -r "@RG\\tID:ILLUMINA-${prefix}\\tSM:${prefix}\\tPL:illumina" $fasta ${prefix}.sai $reads | samtools sort -@ ${task.cpus} -O bam - > "${prefix}".sorted.bam