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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