Merge branch 'documentation_rhea' into 'master'

Rhea naming

Closes #94

See merge request zavolan_group/pipelines/rhea!51

.gitlab-ci.yml

@@ -4,7 +4,7 @@ before_script:
   - apt update && apt install -y gcc
   - conda init bash && source ~/.bashrc && echo $CONDA_DEFAULT_ENV
   - conda env create -f install/environment.root.yml
-  - conda activate rnaseq_pipeline && echo $CONDA_DEFAULT_ENV
+  - conda activate rhea && echo $CONDA_DEFAULT_ENV
   - conda env update -f install/environment.dev.yml
 
 test:

README.md

-# RNA-Seq pipeline
+# Rhea pipeline
 
 [Snakemake][snakemake] workflow for general purpose RNA-Seq library annotation
 developed by the [Zavolan lab][zavolan-lab].
@@ -29,8 +29,8 @@ Traverse to the desired path on your file system, then clone the repository and
 move into it with:
 
 ```bash
-git clone ssh://git@git.scicore.unibas.ch:2222/zavolan_group/pipelines/rnaseqpipeline.git
-cd rnaseqpipeline
+git clone ssh://git@git.scicore.unibas.ch:2222/zavolan_group/pipelines/rhea.git
+cd rhea
 ```
 
 ### Installing Conda
@@ -87,7 +87,7 @@ conda env create -f install/environment.root.yml
 Activate the Conda environment with:
 
 ```bash
-conda activate rnaseq_pipeline
+conda activate rhea
 ```
 
 ### Installing non-essential dependencies

install/environment.dev.yml

-name: rnaseq_pipeline
+name: rhea
 channels:
   - bioconda
   - conda-forge

install/environment.root.yml

-name: rnaseq_pipeline
+name: rhea
 channels:
   - conda-forge
   - defaults

install/environment.yml

-name: rnaseq_pipeline
+name: rhea
 channels:
   - defaults
 dependencies:

pipeline_documentation.md

-# RNAseq pipeline documentation
+# Rhea workflow documentation
 This document describes the individual rules of the pipeline for information purposes. For instructions on installation and usage please refer to the [README](README.md).    
 
 ## Overview