Dev (#292)

* Update README.md * Update filterSNVs.sh * Update filterSNVs.sh add an if/else pattern. if QC don't filter, if not QC filter to heterozygous * add comment and precision grep * hardcode UCSC results read in * standardize the MAE filter * update comment clarity * force no duplicates after splitting * update docs and filterSNV.sh * remove redundant conversion to UCSC style * remove '.' from test * add gene ranges * ranges added * ranges added * fix tests for '.' * Update .gitignore * labels read count ratio fixed * ranges fixed * update authors * Update Datasets.R * fix qc plot * Update DNA_RNA_matrix_plot.R * hpo function bug fixed * mae links and populations fixed * hpo function fixed * mae genes bug fix * Update Results.R * Update Results.R * speed up hpo function * Update Results.R * rmarkdown instead of markdown * Update Results.R * Update test_MAE.py * update conda to mamba install (#289) * update conda to mamba install * bump tMAE Co-authored-by: Smith Nicholas <smith@in.tum.de> * Update requirementsR.txt * Update README.md * Update setup.py Bump 1.1.2 * Update setup.cfg Bump 1.1.2 * Update conf.py * Update __init__.py Bump 1.1.2 * Update cli.py Bump 1.1.2 Co-authored-by: Vicente Yepez <30469316+vyepez88@users.noreply.github.com> Co-authored-by: Smith Nicholas <smith@in.tum.de> Co-authored-by: Vicente <yepez@in.tum.de>
gagneurlab · Feb 4, 2022 · 1cbba5f · 1cbba5f
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diff --git a/README.md b/README.md
@@ -3,15 +3,15 @@
 [![Version](https://img.shields.io/github/v/release/gagneurlab/drop?include_prereleases)](https://github.com/gagneurlab/drop/releases)
 [![Version](https://readthedocs.org/projects/gagneurlab-drop/badge/?version=latest)](https://gagneurlab-drop.readthedocs.io/en/latest)
 
-The manuscript is now available in [Nature Protocols](https://www.nature.com/articles/s41596-020-00462-5). [SharedIt link.](https://rdcu.be/cdMmF)
+The manuscript is available in [Nature Protocols](https://www.nature.com/articles/s41596-020-00462-5). [SharedIt link.](https://rdcu.be/cdMmF)
 
 <img src="drop_sticker.png" alt="drop logo" width="200" class="center"/>
 
 ## Quickstart
 DROP is available on [bioconda](https://anaconda.org/bioconda/drop).
 We recommend using a dedicated conda environment. (installation time: ~ 10min)
 ```
-conda install -c conda-forge -c bioconda drop
+mamba install -c conda-forge -c bioconda drop
 ```
 
 Test installation with demo project

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -23,7 +23,7 @@
 author = 'Michaela Müller'
 
 # The full version, including alpha/beta/rc tags
-release_ = '1.1.1'
+release_ = '1.1.2'
 
 
 # -- General configuration ---------------------------------------------------

diff --git a/drop/__init__.py b/drop/__init__.py
@@ -4,4 +4,4 @@
 from . import utils
 from . import demo
 
-__version__ = "1.1.1"
+__version__ = "1.1.2"
diff --git a/drop/cli.py b/drop/cli.py
@@ -17,7 +17,7 @@
 
 @click.group()
 @click_log.simple_verbosity_option(logger)
-@click.version_option('1.1.1',prog_name='drop')
+@click.version_option('1.1.2',prog_name='drop')
 
 def main():
     pass

diff --git a/drop/requirementsR.txt b/drop/requirementsR.txt
@@ -2,7 +2,7 @@ package	version
 devtools
 gagneurlab/OUTRIDER	1.6.1
 c-mertes/FRASER	1.2.1
-gagneurlab/tMAE	1.0.3
+gagneurlab/tMAE	1.0.4
 VariantAnnotation	
 rmarkdown	
 knitr	

diff --git a/setup.cfg b/setup.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.1.1
+current_version = 1.1.2
 commit = True
 
 [bumpversion:file:setup.py]

diff --git a/setup.py b/setup.py
@@ -21,7 +21,7 @@
 
 setuptools.setup(
     name="drop",
-    version="1.1.1",
+    version="1.1.2",
     author="Vicente A. Yépez, Michaela Müller, Nicholas H. Smith, Daniela Klaproth-Andrade, Luise Schuller, Ines Scheller, Christian Mertes <mertes@in.tum.de>, Julien Gagneur <gagneur@in.tum.de>",
     author_email="yepez@in.tum.de",
     description="Detection of RNA Outlier Pipeline",