From a07e117336f0d65f14354b52a8f39834106981c4 Mon Sep 17 00:00:00 2001
From: Alex Kanitz <alexander.kanitz@unibas.ch>
Date: Fri, 12 Jun 2020 16:22:24 +0200
Subject: [PATCH] docs: rename project/workflow
---
.gitlab-ci.yml | 2 +-
README.md | 8 ++++----
Snakefile | 2 +-
install/environment.dev.yml | 2 +-
install/environment.root.yml | 2 +-
install/environment.yml | 2 +-
pipeline_documentation.md | 2 +-
scripts/prepare_inputs.py | 10 +++++-----
.../{rhea_multiqc_config.py => zarp_multiqc_config.py} | 6 +++---
9 files changed, 18 insertions(+), 18 deletions(-)
rename workflow/scripts/{rhea_multiqc_config.py => zarp_multiqc_config.py} (97%)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 64fdc8f..fe34e07 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 rhea && echo $CONDA_DEFAULT_ENV
+ - conda activate zarp && echo $CONDA_DEFAULT_ENV
- conda env update -f install/environment.dev.yml
test:
diff --git a/README.md b/README.md
index c8dca57..ed3941e 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-# Rhea pipeline
+# ZARP pipeline
[Snakemake][snakemake] workflow for general purpose RNA-Seq library annotation
developed by the [Zavolan lab][zavolan-lab].
@@ -32,8 +32,8 @@ 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/rhea.git
-cd rhea
+git clone ssh://git@git.scicore.unibas.ch:2222/zavolan_group/pipelines/zarp.git
+cd zarp
```
### Installing Conda
@@ -90,7 +90,7 @@ conda env create -f install/environment.root.yml
Activate the Conda environment with:
```bash
-conda activate rhea
+conda activate zarp
```
### Installing non-essential dependencies
diff --git a/Snakefile b/Snakefile
index 450f545..909ad8a 100644
--- a/Snakefile
+++ b/Snakefile
@@ -1117,7 +1117,7 @@ rule prepare_multiqc_config:
workflow.basedir,
"workflow",
"scripts",
- "rhea_multiqc_config.py")
+ "zarp_multiqc_config.py")
output:
multiqc_config = os.path.join(
diff --git a/install/environment.dev.yml b/install/environment.dev.yml
index ab5c30a..3fa2e72 100644
--- a/install/environment.dev.yml
+++ b/install/environment.dev.yml
@@ -1,4 +1,4 @@
-name: rhea
+name: zarp
channels:
- bioconda
- conda-forge
diff --git a/install/environment.root.yml b/install/environment.root.yml
index 7017feb..20075ba 100644
--- a/install/environment.root.yml
+++ b/install/environment.root.yml
@@ -1,4 +1,4 @@
-name: rhea
+name: zarp
channels:
- conda-forge
- defaults
diff --git a/install/environment.yml b/install/environment.yml
index 4fa641a..1f69c61 100644
--- a/install/environment.yml
+++ b/install/environment.yml
@@ -1,4 +1,4 @@
-name: rhea
+name: zarp
channels:
- defaults
dependencies:
diff --git a/pipeline_documentation.md b/pipeline_documentation.md
index 0a29c8c..6dea086 100644
--- a/pipeline_documentation.md
+++ b/pipeline_documentation.md
@@ -1,4 +1,4 @@
-# Rhea: workflow documentation
+# ZARP: workflow documentation
This document describes the individual steps of the workflow. For instructions
on installation and usage please see [here](README.md).
diff --git a/scripts/prepare_inputs.py b/scripts/prepare_inputs.py
index 1efc031..5bcfb9b 100755
--- a/scripts/prepare_inputs.py
+++ b/scripts/prepare_inputs.py
@@ -1,6 +1,6 @@
#!/usr/bin/env python3
-"""Create input table and config for Rhea."""
+"""Create input table and config for ZARP."""
import argparse
from functools import partial
@@ -79,14 +79,14 @@ def parse_cli_args() -> argparse.Namespace:
"--output-table",
type=argparse.FileType('w'),
default="samples.tsv",
- help="output sample table for use in Rhea (default: %(default)s)",
+ help="output sample table for use in ZARP (default: %(default)s)",
metavar="FILE",
)
io.add_argument(
"--config-file",
type=argparse.FileType('w'),
default="config.yaml",
- help="output Snakemake configuration file for use in Rhea (default: "
+ help="output Snakemake configuration file for use in ZARP (default: "
"%(default)s)",
metavar="FILE",
)
@@ -94,7 +94,7 @@ def parse_cli_args() -> argparse.Namespace:
"--output-dir",
type=str,
default=os.getcwd(),
- help="directory to which Rhea results and logs are to be written "
+ help="directory to which ZARP results and logs are to be written "
"(default: %(default)s)",
metavar="DIR",
)
@@ -453,7 +453,7 @@ def expand_path(
def main(args):
"""
- Create input table and config for Rhea.
+ Create input table and config for ZARP.
"""
setup_logging(
logger=logger,
diff --git a/workflow/scripts/rhea_multiqc_config.py b/workflow/scripts/zarp_multiqc_config.py
similarity index 97%
rename from workflow/scripts/rhea_multiqc_config.py
rename to workflow/scripts/zarp_multiqc_config.py
index 89dbfb2..68d2d6c 100644
--- a/workflow/scripts/rhea_multiqc_config.py
+++ b/workflow/scripts/zarp_multiqc_config.py
@@ -3,7 +3,7 @@
# -----------------------------------------------------------------------------
# Author : Maria Katsantoni, Maciek Bak
# Company: Mihaela Zavolan, Biozentrum, Basel
-# This script is part of the Zavolan lab Rhea pipeline.
+# This script is part of the Zavolan lab ZARP pipeline.
# In this script the config file used by multiqc
# (https://multiqc.info) is created.
# -----------------------------------------------------------------------------
@@ -62,9 +62,9 @@ def main():
parser.print_help()
sys.exit(1)
- title = "Rhea"
+ title = "ZARP"
subtitle = "RNA-Seq processing pipeline developed by Zavolan Lab"
- logo_title = 'Rhea'
+ logo_title = "ZARP"
project_type = "Snakemake workflow"
analysis_type = "RNA-seq"
--
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