- Fix spelling of shared SIF directory on biowulf -- it is
/data/CCBR_Pipeliner/SIFswith a lowercase "s" at the end. (#54, @kelly-sovacool) - Enable nextflow timeline & trace reports by default. (#55, @kelly-sovacool)
- CRISPIN is now archived in Zenodo as v1.0.0. You can cite it with https://doi.org/10.5281/zenodo.13844209. (@kelly-sovacool)
- Fix bug in spooker handler. (#49, @kelly-sovacool)
- The pipeline name has been changed from CRUISE 🛳️ to CRISPIN 🍪. (#43, @kelly-sovacool)
- Run spooker on workflow completion.
- Print the recommended citation in bibtex format with
crispin --citation. (#32, @kelly-sovacool) - Fix citation information (#38, @kelly-sovacool)
- Improve the documentation website with a dropdown menu to select which version to view. The latest release is shown by default. (#45, @kelly-sovacool)
- All scripts in the bin directory are now made executable for all users on biowulf (#25).
- Data directories are copied recursively during python package installation (#26).
This is the first release of CRUISE 🎉
- Trim adapters with cutadapt.
- Run mageck count. (#9)
mageck countonly runs if a count table isn't given.
- Optional: run mageck test and mle. (#9)
mageck mleonly runs if a design matrix is given.
- Optional: run drugZ. (#10)
- Optional: run BAGEL2. (#11)
- fc (fold change)
- bf (bayes factor)
- pr (precision recall)
- CLI (#16)
cruise initto initialize a project directory.cruise run--mode slurmto submit a slurm job to biowulf or frce.--main path/to/main.nfto select a different local install of cruise, or specify the repo (CCBR/CRUISE) to get it from GitHub.