Merge pull request #136 from apeltzer/dev

Fix for gffread process

CHANGELOG.md

@@ -2,12 +2,20 @@
 
 ## Version 1.2dev
 
-#### Bug Fixes
-* Fixed conda bug which caused problems with environment resolution due to changes in bioconda [#113](https://github.com/nf-core/rnaseq/issues/113)
-* Remove legacy rseqc `strandRule` config code. [#119](https://github.com/nf-core/rnaseq/issues/119)
+
+#### Pipeline updates
 * Removed some outdated documentation about non-existent features
 * Config refactoring and code cleaning
 * Added a `--fcExtraAttributes` option to specify more than ENSEMBL gene names in `featureCounts`
+* Remove legacy rseqc `strandRule` config code. [#119](https://github.com/nf-core/rnaseq/issues/119)
+* Added STRINGTIE ballgown output to results folder [#125](https://github.com/nf-core/rnaseq/issues/125)
+
+
+
+#### Bug Fixes
+* Fixed conda bug which caused problems with environment resolution due to changes in bioconda [#113](https://github.com/nf-core/rnaseq/issues/113)
+* Fixed wrong gffread command line [#117](https://github.com/nf-core/rnaseq/issues/117)
+* Added `cpus = 1` to `workflow summary process` [#130](https://github.com/nf-core/rnaseq/issues/130)
 
 ## [Version 1.1](https://github.com/nf-core/rnaseq/releases/tag/1.1) - 2018-10-05
 

main.nf

@@ -414,7 +414,7 @@ if(params.gff){
 
       script:
       """
-      gffread  $gff -T -o > ${gff.baseName}.gtf
+      gffread  $gff -T -o ${gff.baseName}.gtf
       """
   }
 }