Merge branch 'master' into dev

gagneurlab · Dec 14, 2022 · cbe7723 · cbe7723
2 parents 2ff8d31 + 33e5114
commit cbe7723
Show file tree

Hide file tree

Showing 7 changed files with 8 additions and 6 deletions.
diff --git a/README.md b/README.md
@@ -16,6 +16,8 @@ We have split the 269 samples from the external counts from fibroblasts strand-s
 
 `Snakemake v.7.8` introduced some changes in which changes in parameters can cause rules to be re-executed. More info [here](https://github.com/snakemake/snakemake/issues/1694). This affects DROP and causes certain rules in the AS and QC modules to be triggered even if they were already completed and there were no changes in the sample annotation or scripts. The workaround is to run DROP by adding the parameter `--rerun-triggers mtime`, e.g. `snakemake -n --rerun-triggers mtime` or `snakemake --cores 10 --rerun-triggers mtime`. We will investigate the rules in DROP to fix this.
 
+Version 1.2.4 fixes some critical bugs that affected the performance of the `mae` pipeline, and introduces the `yieldSize` config variable to control batch size when reading BAM files and VCF files for the `aberrantExpression` and `rnaVariantCalling` modules.
+
 Version 1.2.3 fixes a bug in one of the plots in the AE Summary Script as well as simplifies the plots. In addition, there's a new heatmap in the sampleQC Summary that allows to better identify DNA-RNA mismatches.
 
 Version 1.2.2 fixes some critical bugs that affected the performance of the `aberrantExpression` pipeline, and allows sample IDs to be numeric.

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_ = '1.2.3'
+release_ = '1.2.4'
 
 
 

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -21,7 +21,7 @@ Install the current version and use the full path in the following command to in
 
 .. code-block:: bash
 
-    mamba env create -f DROP_1.2.3.yaml
+    mamba env create -f DROP_1.2.4.yaml
 
 Installation time: ~ 10min
 

diff --git a/drop/__init__.py b/drop/__init__.py
@@ -4,5 +4,5 @@
 from . import utils
 from . import demo
 
-__version__ = "1.2.3"
+__version__ = "1.2.4"
 
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('1.2.3',prog_name='drop')
+@click.version_option('1.2.4',prog_name='drop')
 
 
 def main():

diff --git a/setup.cfg b/setup.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.2.3
+current_version = 1.2.4
 commit = True
 
 [bumpversion:file:setup.py]

diff --git a/setup.py b/setup.py
@@ -21,7 +21,7 @@
 
 setuptools.setup(
     name="drop",
-    version="1.2.3",
+    version="1.2.4",
 
     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",