diff --git a/README.md b/README.md index 152f9d3e..9d5ebab9 100644 --- a/README.md +++ b/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. diff --git a/docs/source/conf.py b/docs/source/conf.py index 80980cbb..8b0f5e64 100644 --- 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_ = '1.3.0' +release_ = '1.3.1' diff --git a/docs/source/installation.rst b/docs/source/installation.rst index 38ac82e3..46cd0c32 100644 --- a/docs/source/installation.rst +++ b/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 diff --git a/drop/__init__.py b/drop/__init__.py index af2d5577..92d94330 100644 --- a/drop/__init__.py +++ b/drop/__init__.py @@ -4,5 +4,5 @@ from . import utils from . import demo -__version__ = "1.3.0" +__version__ = "1.3.1" diff --git a/drop/cli.py b/drop/cli.py index 30158b6b..9dc6b41f 100644 --- a/drop/cli.py +++ b/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(): diff --git a/setup.cfg b/setup.cfg index 682ae132..43c0dbce 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.3.0 +current_version = 1.3.1 commit = True [bumpversion:file:setup.py] diff --git a/setup.py b/setup.py index 663c16f8..323297f5 100644 --- a/setup.py +++ b/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 , Julien Gagneur ", author_email="yepez@in.tum.de",