« Changelog History


bcbio-nextgen v1.1.4 Release Notes

Release Date: 2019-04-03 // about 5 years ago
    • 🚚 Move to Python 3.6. A python2 environment in the install runs non python3 compatible programs. The codebase is still compatible with python 2.7 but will only get run and tested on python 3 for future releases.
    • RNA-seq: fix for race condition when creating the pizzly cache
    • RNA-seq: Add Salmon to multiqc report.
    • RNA-seq single-cell/DGE: Properly strip transcript versions from GENCODE GTFs.
    • RNA-seq: Faster and more flexible rRNA biotype lookup.
    • ⚡️ Move to R3.5.1, including updates to all CRAN and Bioconductor packages.
    • tumor-only germline prioritization: provide more useful germline filtering based on prioritization INFO tag (EPR) rather than filter field.
    • Install: do not require fabric for tool and data installs, making full codebase compatible with python 3.
    • variant: Filter out variants with missing ALT alleles output by GATK4.
    • GATK: enable specification of spark specific parameters with gatk-spark resources.
    • RNA-seq single-cell/DGE: added demultiplexed option. If set to True, treat the data as if it has already been demultiplexed into cells/wells.
    • Multiple orders of magnitude faster templating with thousands of input files.