grenepipe v0.2.0

Official release for the arXiv manuscript describing grenepipe:

Lucas Czech, Moises Exposito-Alonso.
grenepipe: A flexible, scalable, and reproducible pipeline to automate variant and frequency calling from sequence reads.
arXiv. 2021.
arXiv:2103.15167

Notable Changes

• Refine helper scripts for sample table generation and for FTP download
• Improve documentation in Wiki
• Better parallelization of FreeBayes
• Add Picard CollectMultipleMetrics QC statistics
• Add samtools view filtering step after mapping
• Add frequency table output

Bug Fixes

• Fix freebayes threads counting
• Fix fastqc rule based on wrapper issue
• Fix vcfpy version parsing issue
• Fix gzip compression issue in prep rule
• Fix slurm submission log file path setup

grenepipe v0.1.0

Initial release of grenepipe. Has sufficient documentation to get it working (hopefully), is stable enough for production (presumably), but still contains bugs (probably), and needs more features (definitely).