Merge pull request #448 from gagneurlab/dev

version nr update after minor change

README.md

@@ -12,7 +12,7 @@ The manuscript is available in [Nature Protocols](https://www.nature.com/article
 
 ## What's new
 
-Version 1.3.0 introduces the option to use FRASER 2.0 which is an improved version of FRASER that uses the Intron Jaccard Index metric instead of percent spliced in and splicing efficiency to quantify and later call aberrant splicing. To run FRASER 2.0, modify the `FRASER_version` parameter in the aberrantSplicing dictionary in the config file and adapt the `quantileForFiltering` and `deltaPsiCutoff` parameters. See [config template](https://github.com/gagneurlab/drop/blob/master/drop/template/config.yaml).
+Version 1.3.0 introduces the option to use FRASER 2.0 which is an improved version of FRASER that uses the Intron Jaccard Index metric instead of percent spliced in and splicing efficiency to quantify and later call aberrant splicing. To run FRASER 2.0, modify the `FRASER_version` parameter in the aberrantSplicing dictionary in the config file and adapt the `quantileForFiltering` and `deltaPsiCutoff` parameters. See [config template](https://github.com/gagneurlab/drop/blob/master/drop/template/config.yaml). Moreover, it allows to provide lists of genes to focus on and do the multiple testing correction instead of the usual transcriptome-wide approach. Refer to the [documentation](https://gagneurlab-drop.readthedocs.io/en/latest/prepare.html#limiting-fdr-correction-to-subsets-of-genes-of-interest).
 
 `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.
 

docs/source/conf.py

@@ -23,7 +23,7 @@
 author = 'Michaela Müller'
 
 # The full version, including alpha/beta/rc tags
-release_ = '1.3.0'
+release_ = '1.3.1'
 
 
 

docs/source/installation.rst

@@ -20,7 +20,7 @@ Install the latest version and use the full path in the following command to ins
 
 .. code-block:: bash
 
-    mamba env create -f DROP_1.3.0.yaml
+    mamba env create -f DROP_1.3.1.yaml
 
 Installation time: ~ 10min
 

drop/__init__.py

@@ -4,5 +4,5 @@
 from . import utils
 from . import demo
 
-__version__ = "1.3.0"
+__version__ = "1.3.1"
 

drop/cli.py

@@ -17,7 +17,7 @@
 
 @click.group()
 @click_log.simple_verbosity_option(logger)
-@click.version_option('1.3.0',prog_name='drop')
+@click.version_option('1.3.1',prog_name='drop')
 
 
 def main():

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.3.0
+current_version = 1.3.1
 commit = True
 
 [bumpversion:file:setup.py]

setup.py

@@ -21,7 +21,7 @@
 
 setuptools.setup(
     name="drop",
-    version="1.3.0",
+    version="1.3.1",
 
     author="Vicente A. Yépez, Michaela Müller, Nicholas H. Smith, Daniela Klaproth-Andrade, Luise Schuller, Ines Scheller, Christian Mertes <[email protected]>, Julien Gagneur <[email protected]>",
     author_email="[email protected]",