bcbio-nextgen v1.2.8 Release Notes

Release Date: 2021-04-14 // 7 months ago
    • Set ENCODE library complexity flags properly for ChIP-seq. Thanks to @mistrm82.
    • ๐Ÿ›  Fix greylisted peaks not being propagated to the output directory. Thanks to @mistrm82.
    • ๐Ÿ‘ Better error message when no sample barcodes are found for single-cell RNA-seq.
    • ๐Ÿ‘ Better trimming for 2 wgbs kits
    • enable setting parameters for deduplicate_bismark
    • custom threading for bismark via yaml
    • reproducible WGBS user story with the data from Encode
    • While consensus peak calling, keep the highest scoring peak instead of calling the summit for the highest scoring peak and expanding the peak to 250 bases.
    • Enable consensus peak calling for broad peaks. Thanks to @mistrm82 and @yoonsquared for pointing out this was missing.
    • โœ… Re-enable ATAC-seq tests, they work now.
    • svprioritize for mm10
    • ๐Ÿš€ purecn_Dx.R - mutational signatures - still requires a manual update of deconstructsigs or release of it
    • ๐Ÿ‘‰ make sure purecn uses sv_regions bed to call variants
    • ๐Ÿ›  fix misleading disambiguation fastqc read statistics (total, hg38, mm10)
    • wgbs: nebemseq kit: add --maxins 1000 and --local to bismark align
    • WGBS: sorted indexed deduplicated bam for ready.bam
    • ๐Ÿ–จ print error message when aligner: false and hla typing is on
    • ๐Ÿ‘‰ make sure that mark_duplicates is false with collapsed UMI input

Previous changes from v1.2.7

    • RNASeq: Add gene body coverage plots to multiqc report.
    • โช Restore ability to opt out of contamination checking via tools_off.
    • Properly invoke threading for verifybamid2.
    • ๐Ÿ›  Fix circular import issue when using bcbio functions outside of the main bcbio script.
    • Enable setting custom PureCN options via YAML file.