New Features
- bcftools stats for each caller #366
- Support for fasterq
- Metrics workflow
- New PCR-free workflows #384
- Illumina expansion hunter
- Constitutional gatk_cnv
- Very similar to the tumor only workflow
- tHReD workflow #432
CMD Changes - Will cause restarts
- Cellranger has been updated to v6.0.1, includes updated changes for fastq naming and expected number of cells #403, #166
- Updated md5sum bam/cram generation for better pathing #425
- stats2json and stats2lims workflow fix for bam level jsons #418
- Only will cause restarts for bam_qc_all jsons
- Summarize_mm_igtx will now have a constant number of columns depending on the number of callers and genes #415
- mm_igtx_gammit
- Updated workflow to reduce variability in alignments and updated script for processing the assembled bam
- Fixed output of annotSeg.pl to properly header the seg.vcf file and give proper calcuation for the SVLEN
Task flow changes
- Modified fastq tracking for salmon, no change in render though