1.1.4 (2024-08-06)
- upload schema.svg (675f4de)
1.1.3 (2024-08-06)
- update profile with better values (9c9e80e)
1.1.2 (2024-06-06)
1.1.1 (2024-06-06)
- infer properly sex chromosomes when only one is in the reference (e89e48c)
- put all rule on top of cache (d404cb6)
1.1.0 (2024-05-13)
- correct input for metarule align__index (37fbc97)
- add align and genotype groups (9510d65)
- add bedtools (9df30a5)
- add groups (462e389)
- add more chromosomes to mock data (c500757)
- add preliminary bcftools calls for gatk (7db0528)
- add resources to the new rules that seem to work at least in a macro level (30829d2)
- add somalier execution + reports (0ea0640)
- add swaps checkpoint (80e7758)
- Added sommalier steps. Will try to figure it out how it works in mice (#8) (3ceb0a9)
- bowtie2 -> bwa (005cc35)
- convert markduplicates to cram (a282483)
- disable swaps (f008602)
- do vep annotation by sample (a7dfd4d)
- Document all functions and rules (#10) (265aeb6)
- Fix versions (#4) (48689dc)
- gtcheck, fastp reports, cache misses (#18) (ca99476)
- i don't remember (f82ed90)
- little turds (#13) (5920444)
- Little turds part 2 (#14) (cac2932)
- merge align bams into a single cram (2d8d4bc)
- merge align reports by sample-library, rather than sample-library-chromosome (0f1a550)
- merge libraries into sample in markduplicates (323837b)
- merge libraries into sample in reports (cd985fd)
- minimum viable product (#1) (407fa5d)
- picard and gatk analyses and reports by chromosome (#7) (d443110)
- pin bwa version (0df670a)
- process samples in haplotype caller (363cbcd)
- process samples in recalibrate (a50704c)
- process stuff in bed4 file (42d1e84)
- raise slurm latency (#9) (6d1388c)
- recalibrate with cram as input and output (f718d0e)
- remove fastp step (6ae55f0)
- Reports by chromosome (#11) (9fe72f1)
- Reports per step and per sample (#3) (a81afe5)
- separate indel and snps, then merge; major rewrite (5613d8f)
- set threads to 0 in mark duplicates and apply bsqr since the hard work is done by samtools (22c838b)
- Set up cache (#12) (e6e2366)
- sex-dependent ploidy (#17) (295065e)
- Slurm-ready (#5) (d7bbd38)
- substitute picard for gatk4 (d622d7c)
- update .gitignore (1c76647)
- update environments, update pre-commit (b0de86e)
- use bwa-mem2 (0f29b48)
- add environment (8106036)
- add Illumina universal adapters (baedd26)
- add mock bed file (ab23d03)
- add mock gtf (19147c6)
- add somalier to env (3d6f2ed)
- add tbi files (6a6b8a1)
- add tmp folder for mark_duplicates (77424d6)
- disable level (cbbd1b5)
- disable max_threads (aa54952)
- disable snpeff (25b3cbf)
- do not ignore resources (ad06ced)
- do not include preprocess (fc74451)
- fastp + gha (#16) (c735460)
- fix downstream side-effects in all rules (808b49e)
- generate mock vcf file when the chromosome is not present in the sample (70f6bb5)
- give vep reports a name that multiqc can recognize (4b9a6d7)
- I should test more often (a96251a)
- limit fastp to 16 threads (#20) (8144bcb)
- remove minimizer sort (506a8de)
- safety check to convert fasta to bed4 (22db278)
- Slurm times + weekly cache (#15) (5c91a49)
- snpeff download db (c55da24)
- sort gtf with bedtools (fb2eab5)
- update documentation (#19) (44a33cd)