From b1f10e9ef9829475940740f4104550f4206e5be9 Mon Sep 17 00:00:00 2001
From: BIOPZ-Katsantoni Maria <maria.katsantoni@unibas.ch>
Date: Thu, 19 Mar 2020 09:49:21 +0100
Subject: [PATCH] Rename pipeline

---
 .gitlab-ci.yml               | 2 +-
 README.md                    | 8 ++++----
 install/environment.dev.yml  | 2 +-
 install/environment.root.yml | 2 +-
 install/environment.yml      | 2 +-
 pipeline_documentation.md    | 2 +-
 6 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 0b9cc41..771bf2b 100644
--- a/.gitlab-ci.yml
+++ b/.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:
diff --git a/README.md b/README.md
index 3c966b4..c4c3292 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-# 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
diff --git a/install/environment.dev.yml b/install/environment.dev.yml
index ea44dfb..ab5c30a 100644
--- a/install/environment.dev.yml
+++ b/install/environment.dev.yml
@@ -1,4 +1,4 @@
-name: rnaseq_pipeline
+name: rhea
 channels:
   - bioconda
   - conda-forge
diff --git a/install/environment.root.yml b/install/environment.root.yml
index 9c6d56d..7017feb 100644
--- a/install/environment.root.yml
+++ b/install/environment.root.yml
@@ -1,4 +1,4 @@
-name: rnaseq_pipeline
+name: rhea
 channels:
   - conda-forge
   - defaults
diff --git a/install/environment.yml b/install/environment.yml
index dd6b5d5..4fa641a 100644
--- a/install/environment.yml
+++ b/install/environment.yml
@@ -1,4 +1,4 @@
-name: rnaseq_pipeline
+name: rhea
 channels:
   - defaults
 dependencies:
diff --git a/pipeline_documentation.md b/pipeline_documentation.md
index 18a6488..4491842 100644
--- a/pipeline_documentation.md
+++ b/pipeline_documentation.md
@@ -1,4 +1,4 @@
-# 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
-- 
GitLab