GitLab

* 12 months ago it worked, maybe it was 4.7.12?

* removed r channel in dockerfile

* won't work fom quay, since image only builds after release

Fix on general report columns

* added option for "no differential expression" information retrieval

Data is now grouped again by Entry before generating expression_matrix, because COGs expand it, making duplicate row names

If CDD has already been downloaded, it won't download it again, nor other reCOGnizer's resources

Removed trimming of last 2 characters in read fixing after rRNA removal

* and other messed reads
* in rRNA removal

closes #13

* MOSCA is now capable of running MT without MG
* Combined with approach to not use assembly
* In the future might implement the use of assembly to analyze MT
Also added rejected and accepted files from rRNA removal to list of files to delete at preprocessing

closes #3

* now reaches annotation
MOSCA no longer overwrites experiments file (which was dumb)
Made option to NOT download UniProt functional
Upped version of reCOGnizer to 1.4

Also updated config to new version

* scripts folder in join_information fixed
* IMPORTANT: fixed removing original files in rRNA removal!

* because of new version of reCOGnizer
* because of Rscript not being the env's

* also fixed bug when using SE data

* Added R script for proteomics postprocessing - imputation and normalization
* MS convert handling accepts no use of peak picking
* Changes to methods for generation of 2nd search database
* Also added the handling of different options to "do_assembly"
* and added "--printshellcmds"