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Fix for gffread process #136

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merged 3 commits into from
Dec 12, 2018
Merged

Fix for gffread process #136

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95afb68
Fix for gtfread
apeltzer Dec 12, 2018
137c066
More changes in changelog
apeltzer Dec 12, 2018
bbdf096
Nicer changelog
apeltzer Dec 12, 2018
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14 changes: 11 additions & 3 deletions CHANGELOG.md
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Expand Up @@ -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* Removed some outdated documentation about non-existent features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

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2 changes: 1 addition & 1 deletion main.nf
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Expand Up @@ -414,7 +414,7 @@ if(params.gff){

script:
"""
gffread $gff -T -o > ${gff.baseName}.gtf
gffread $gff -T -o ${gff.baseName}.gtf
"""
}
}
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