v0.3.3

This release patches an issue with VarDict's handling of IUPAC ambiguity codes and "dup" strings in its ALT alleles. See issue #42 for a description of the resolved bug. Thanks to @elahoehne for reporting!

v0.3.1

Our paper is out! So this release just adds citation information to our README file. In addition, we created a CITATION.cff file so that Github can parse the citation info in a machine-readable format.

v0.3.0

This release brings improved reproducibility for those using --use-conda by including exact channel specifications in the conda environment files. It also adds a few more common packages (like bash) to the environment files in order to override whichever version is pre-installed. See #32 for more info.

v0.2.3

Fixes an issue where the tsv2vcf Snakemake rule within the classify subworkflow would occasionally fail because of a non-zero exit code from zcat because of 2vcf.py. See #28 for more details.

v0.2.2

This release patches an issue with VarScan's handling of IUPAC ambiguity codes. See issue #25 for a description of the resolved bug, which appears when using specific reference genomes like hs37d5. Thanks to @lindenb for reporting!

Improved Documentation

This release updates README files across the repository in an effort to improve our documentation.

1. The main README provides just enough information for those who want to run the pipeline on the example data.
2. The config.yaml section of the config README instructs users on how to execute the pipeline on their own data.
3. The rest of the config README and the rules README tells them how to run the "prepare" and "classify" subworkflows separately from the master pipeline. It also instructs users on how to reproduce our results.
4. Add to that the callers README, and they should be able to try their own variant callers.
5. And the comments within the config files provide everything anyone could possibly want to know.

New VCF Output

The most notable change in this release is that the pipeline now produces VCF output.
However, there are a number of other minor changes which generally make the pipeline easier to use. For more information see pull request #16.

Initial Release

Initial release. Users can now run the pipeline on example data.