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COMBAT-TB / irida-pipeline-plugins

Galaxy pipelines as plugin for IRIDA intergration
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Enhancements to TB phylogeny pipeline #11

Closed pvanheus closed 3 years ago

pvanheus commented 3 years ago

As I am reviewing the TB phylogeny pipeline I am noting some issue that should be corrected:

  1. SnpEff should be removed as we do not need to annotate these variants
  2. a SNP matrix should be produced using snp-dists (https://toolshed.g2.bx.psu.edu/repository?repository_id=a069dc7e9be1ee39&changeset_revision=1959cc43b414)
pvanheus commented 3 years ago

I addressed 1, 2 and the enhancement requested in [#12] in the workflow here: https://gist.github.com/pvanheus/0d02e29cca7f473e0f5b9b3f7d949a86

This should be incorporated into a new version of the IRIDA workflow.