Fixed custom output folder for compute transcriptome
fixed issue with single end reads and ID cleanup (#9)
Merge branch 'v1.7.1' into develop

Conflicts:
	Readme.md
updated readme
Merge branch 'v1.7.1' into develop
added coverage stats calculation to gtfstats run in rnaseq pipeline
fixed sam test and added -p parameter
Fixed typo
bumped version
Merge branch 'v1.7.1'
merged after 1.7.1 release
bumperd download link in readme
merged readme upload link fix