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add a sourmash module

Open fmalmeida opened this issue 3 years ago • 1 comments

Add an additional module for scanning the sample using sourmash:

  • [x] scan against refseq using whole genome (LCA)
  • [x] an option to create a simple phylogeny using sourmash against the N closest genomes detected in the pipeline using refseq_masher module or against genomes provided by user in a directory
  • [ ] Include results in HTML reports

fmalmeida avatar Oct 30 '21 21:10 fmalmeida

Just missing addition in the reports.

fmalmeida avatar May 31 '23 10:05 fmalmeida

Module working fine in workflow. HTML reports containing desired results. Missing:

  • [x] publish docker image
  • [x] generating and publishing new pre-built database
  • [x] updating HTML reports examples in documentation for new ones with sourmash

fmalmeida avatar Jul 06 '24 16:07 fmalmeida

Finally opened PR for final review before releasing: https://github.com/fmalmeida/bacannot/pull/125

fmalmeida avatar Jul 06 '24 20:07 fmalmeida