1.1.0 (2024-03-12)
- containerize pipeline's output (a3b4086)
- enable caching for all references and STAR indexes (bc99687)
- test Snakemake report generation (c2c0f46)
- update Dockerfile (bb47f34)
- add singularity-args and reformat lines in CI (598de8d)
- cleanup Snakemake test profile (2c2cdf7)
- formatting edit_condition_file.py (e26f101)
- properly download using UCSC API. Fix all paths and enable caching (db8da50)
- switch to wget and write some logging when downloading genome annotations (c49e4ff)
1.0.1 (2024-03-06)
- add example Slurm configuration (96ce038)
- decouple TE, tRNA and single copy genes pipelines. Allow users to decide which branches to run.#3 (d3b12e4)
- describe how to run tests (46e023f)
- DESeq2 reference is now separate for each sequencing library (b4cf102)
- allow deseq2 ananlysi with different variables and different levels (76c2562)
- fix deseq2 scripts to look for correct column names (ffc4537)
- fix problem with SalmonTE quant input array on single-end libraries (3fd51ff)
- fix Snakemake version to be below 8 (5fa9be3)
- look for correct column name in edit_conditions_file.py (e60456e)
- make test dataset smaller to let it run in GH Actions (17ac70d)
- pin all conda packages versions (feddd48)
- remove params.mem_mb from starTE rules (b6f1848)
- restore test profile (c50b75e)
- revert alpine base for SalmonTE Docker (bfb4a48)
- switch to miniconda3-alpine as base (7ac38c7)
- test config now has library-specific deseq2 reference level (44d4b43)
- typo (6e64c84)
- update docs (c811991)
- release 1.0.1 (25c11bc)
- add file for Snakemake workflow catalog (cf8723d)
- add pseudocounts to count matrix if cannot estimate size factors (219d665)
- explicit all star outputs (2f2d7b9)
- start basic documentation (1d57ff5)
- update Dockerfile (877bf88)
- add tests (418381b)
- add text data (328781a)
- config directory (bbf4926)
- correctly pass genome label to get_rmsk.py (8157a11)
- edit_condition_file rule (adb0a5e)
- mkdir (646a3d4)
- mv configuration docs to specific README file (a8adec4)
- pin R version for SalmonTE (b7c238b)
- polish (5d4b3b7)
- remove useless print (fa11e58)
- snakemake variable (a123c63)
- syntax (1d20176)
- update TOKEN in main CI workflow (3d9faaa)