bcbio-nextgen v1.2.9 Release Notes
Release Date: 2021-12-14 // over 2 years ago-
- 🛠 Fix vcf header bug: T/N SAMPLE lines are back - needed for import to SolveBio
- ➕ add strandedness: auto for -l A option in salmon
- report 10x more peaks in CHIP/ATAC-seq - use 0.05 qvalue
- 🛠 fix misleading RNA-seq duplicated reads statistics: thanks @sib-bcf
- reorganize conda environments
- snpEff 5.0
- strandedness: auto
- document WGBS pipeline steps
- 0️⃣ make --local an option, not default in bismark alignment - too slow
- ⚡️ bcbioRNASeq update to 0.3.44
- ⚡️ pureCN update to 2.0.1
- ⚡️ octopus update to 0.7.4
Previous changes from v1.2.8
-
- 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