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.