Change Log

2.0

Substantial performance improvements were achieved by applying parallelization strategies to additional steps of the workflow.

  • A new Snakefile for OVarFlow 2.0 was created, rearranging the workflow (CombineGVCFs and GenotypeGVCFs were both parallelized).

  • Preexisting GVCF files won’t be used by OVarFlow 2.0.

  • Comprehensive documentation of OVarFlow 2.0 was created.

  • Flowchart comparing OVarFlow 1 and OVarFlow 2 was added to the documentation.

  • Benchmarking to compare the performance of OVarFlow 1 and 2.

1.2.0

  • Improved scheduling of bwa memory usage (especially useful for Slurm).

  • Documentation for bwa memory scheduling added.

  • Improved documentation for memory scheduling via config.yaml.

  • Two new alternative target rules added to the workflow.

  • Documentation provided for these new target rules.

  • Minor corrections to the documentation, such as typos and wording.

1.1.0

  • Improved scheduling of memory usage (especially useful for Slurm usage).

  • Documentation for Slurm usage added.

  • Java memory overhead enabled for better resource scheduling (affects Snakefile, config.yaml and documentation).

  • Some refactoring of the Snakefile (mainly formatting).

  • Change log added to documentation.

  • Citation of final publication added.

1.0.1

Various improvements were added to the documentation. No changes to the workflow.

  • New section about error identification added.

  • Better explanation of snakemake options -j and –cores.

  • bioRxiv link added.

  • Small fixes, like typos.

1.0

  • Initial release of OVarFlow, including the “normal” variant calling workflow and the optional BQSR workflow.