Skip to content

v1.6.0
Compare
Choose a tag to compare
@jaleezyy jaleezyy released this 17 Mar 18:56
· 35 commits to master since this release
v1.6.0
f66f2f7
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Learn about vigilant mode.

Major updates to SIGNAL execution:

  • signal.py has been renamed to signalexe.py
  • signalexe.py install option allows for per-rule environment installation without requiring input data (future versions will include testing using curated data)
  • --data flag added to allow you to specify the location of file data dependencies
  • Additional snakemake parameters have been added as options for signalexe.py including: --ignore-incomplete and --quiet

General updates:

  • Improved handling of failed samples that would otherwise produce snakemake errors. Samples that fail assembly will be logged within a new output file: failed_samples.log, found within the results directory
  • Improved linking of prerequisite files for ncov-tools (when executing signalexe.py ncov_tools) where failed samples will be excluded to minimize errors
  • Nextclade dataset download now skippable if provided version (within configuration file) matches one already found within scripts/nextclade. This also makes the lineage assignment portion of SIGNAL more offline-friendly as SIGNAL will use whichever datasets are available within scripts/nextclade if it cannot update. This updating now follows the same logic as Pangolin and Nextclade updating
  • Updates to per-rule conda environments to remove stale packages

Additional (optional) scripts:

  • General extraction script (scripts/get_signal_results.sh) provided which can be used to pull consensus, variant, and select reports from SIGNAL + ncov-tools
Assets 2
Loading