Customizable workflows based on snakemake and python for the analysis of NGS data
Full Changelog: https://github.com/maxplanck-ie/snakepipes/compare/2.8.0...2.8.1
snakePipes 2.7.2
STAR version has been updated to 2.7.10b. 2.7.10a was returning segmentation fault on MAC.
STAR command has been updated. Now, STAR itself offers a command line option for processing input files.
Put a cap on python version for the deeptools env. The current version of deeptools is not supporting the newer python versions and some tools fail.
Update default condaDir.
The filter_gtf function has become a bit more versatile. GTF files that include delimiters (';') in e.g. a description field are now allowed. Gene names are also allowed to have symbols now. Lastly, GTF files that have xRNA instead of transcript as a feature in column 3 can also be parsed.
Full Changelog: https://github.com/maxplanck-ie/snakepipes/compare/2.7.0...2.7.2
snakePipes 2.5.4
Fixed a number of minor GitHub issues: #791, #816, #807, #789, #783, #768, #827.
Fixed misleading rule name for bamcoverage in atac-seq.
Fixed conda env building on microsoft azure.
Fixed CSAW report for ChIP-seq.
createEnvs
function.