Set ENCODE library complexity flags properly for ChIP-seq. Thanks to @mistrm82. Fix greylisted peaks not being propagated to the output directory. Thanks to @mistrm82. Better error message when no sample barcodes are found for single-cell RNA-seq. 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. Re-enable ATAC-seq tests, they work now. svprioritize for mm10 purecn_Dx.R - mutational signatures - still requires a manual update of deconstructsigs or release of it make sure purecn uses sv_regions bed to call variants 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 print error message when aligner: false and hla typing is on make sure that mark_duplicates is false with collapsed UMI input