NGI-RNAseq v1.4

The version 1.4 release contains major improvements to the NGI-RNAseq pipeline, especially focussed on the portability of the pipeline. Hopefully these changes will make it significantly easier for people to use the pipeline in different compute environments.

Many thanks to everyone who gave us feedback about the pipeline!

• Changed default config to base instead of uppmax
  • UPPMAX users now need to specify -profile uppmax
• Removed default reverse stranded config for UPPMAX profile
  • UPPMAX users now need to specify --reverse_stranded for the same behaviour
• Added an environment.yml file to easily create a (bio)conda environment for the pipeline
• Rewrote the Dockerfile to build the docker container using conda
• Switched UPPMAX configuration to use Singularity instead of environment modules
• Switched c3se Hebbe configuration to use Singularity & refactored config
• Added config profiles for two clusters at QBiC in Tübingen, Germany
• Made output from DupRadar, Biotype Counts and edgeR sample similarity use MultiQC Custom Content formatting
  • These results now show up in MultiQC reports for everyone, not just people with our custom MultiQC plugin
• Reorganised and rewrote much of the documentation
• Added a Troubleshooting section to the docs
• Fixed bug where BED12 generation failed when only GTF supplied.
• Changed dupradar script to use number of threads defined by nextflow process
• Fixed call to dupradar script that prevented interpretation of paired-ends reads and strand direction