Rna-count-salmon

News

- Unique [CLI](https://en.wikipedia.org/wiki/Command-line_interface) launcher: rna-count-salmon.py
- Setup for pipy

Updates

- Conda env updates

Flamingo

Reviewed and tested by flamingo user at IGR

Updates:

- Snakemake, SnakemakeWrappers & Python
- Snakemake linter passed
- Black with py38 and line length of 80 passed

Fall back:

- No more notebook
- Graphs removed
- No more custom multiqc

New features

- MultiQC customisation
- QC graph on null counts
- QC graph on count quartiles

Updates

- Logging behaviour improved
- Removed unnecessary rule links
- Removed unnecessary files in "all" rule
- New temp flags

Changes

- Multiple changes in Make options

Minor changes in the report

Updates

* Snakemake and its wrappers were updated
* New report content
* Global environment updated

Rulegraph

* Now included in the readme: use `make workflow.png` to get it
* DAG also available with: `make example.png`