crispin - CRISPIN 1.2.0

• CRISPIN now depends on ccbr_tools v0.4 for updated jobby & spooker utilities. (#63, @kelly-sovacool)

- Nextflow
Published by github-actions[bot] about 1 year ago

crispin - CRISPIN 1.1.1

• Fix error in spooker usage. (#61, @kelly-sovacool)
• Bump ccbr_tools to v0.3

- Nextflow
Published by github-actions[bot] about 1 year ago

crispin - CRISPIN 1.1.0

• CLI updates: (#58, @kelly-sovacool)
  • Use nextflow run -resume by default, or turn it off with crispin run --forceall.
  • Add --output argument for crispin init and crispin run.
  • If not provided, commands are run in the current working directory.
  • This is equivalent to the nextflow $launchDir constant.
  • The nextflow preview is printed before launching the actual run.
• Nextflow updates:
  • Enable nextflow timeline & trace reports by default. (#55, @kelly-sovacool)
  • Set the publish_dir_mode nextflow option to link by default. (#58, @kelly-sovacool)
  • Set the process.cache nextflow option to deep by default on biowulf. (#58, @kelly-sovacool)
• Minor documentation updates. (#57, @kelly-sovacool)
• Fix spelling of shared SIF directory on biowulf -- it is /data/CCBR_Pipeliner/SIFs with a lowercase "s" at the end. (#54, @kelly-sovacool)

- Nextflow
Published by github-actions[bot] about 1 year ago

crispin - CRISPIN 1.0.1

• 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)

- Nextflow
Published by github-actions[bot] over 1 year ago

crispin - CRISPIN 1.0.0

• 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)

Full Changelog: https://github.com/CCBR/CRISPIN/compare/v0.1.1...v1.0.0

- Nextflow
Published by kelly-sovacool over 1 year ago

crispin - CRUISE 0.1.1

Bug fixes

• 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).

Full Changelog: https://github.com/CCBR/CRUISE/compare/v0.1.0...v0.1.1

- Nextflow
Published by kelly-sovacool over 2 years ago

crispin - CRUISE 0.1.0

This is the first release of CRUISE 🎉

New features

• Trim adapters with cutadapt.
• Run mageck count. (#9)
  • mageck count only runs if a count table isn't given.
• Optional: run mageck test and mle. (#9)
  • mageck mle only 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 init to initialize a project directory.
  • cruise run
  • --mode slurm to submit a slurm job to biowulf or frce.
  • --main path/to/main.nf to select a different local install of cruise, or specify the repo (CCBR/CRUISE) to get it from GitHub.

- Nextflow
Published by kelly-sovacool over 2 years ago