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Recent Releases of poppipe

poppipe - PopPIPE v1.2.0

Added various changes suggested by paper review, including edge case fixes and more output from the transmission steps.

What's Changed

  • Update Snakefile by @qtoussaint in https://github.com/bacpop/PopPIPE/pull/18
  • Update number_clusters.py by @sbenvari in https://github.com/bacpop/PopPIPE/pull/21
  • Deal with merged cluster names in group_stragglers by @johnlees in https://github.com/bacpop/PopPIPE/pull/23
  • Update and simplify installation instructions by @johnlees in https://github.com/bacpop/PopPIPE/pull/24

New Contributors

  • @qtoussaint made their first contribution in https://github.com/bacpop/PopPIPE/pull/18
  • @sbenvari made their first contribution in https://github.com/bacpop/PopPIPE/pull/21

Full Changelog: https://github.com/bacpop/PopPIPE/compare/v1.1.0...v1.2.0

- Python
Published by johnlees 12 months ago

poppipe - PopPIPE v1.1.0

Use ska.rust instead of ska and add the transmission target

What's Changed

  • Fix for when hashes in file name by @johannahelene in https://github.com/bacpop/PopPIPE/pull/9
  • Adding transphylo, gubbins, bactdating by @johannahelene in https://github.com/bacpop/PopPIPE/pull/10
  • Try to catch tiny alignments, output no further subclusters by @johnlees in https://github.com/bacpop/PopPIPE/pull/12
  • Replace ska with ska.rust, add transmission pipeline by @johnlees in https://github.com/bacpop/PopPIPE/pull/16

New Contributors

  • @johannahelene made their first contribution in https://github.com/bacpop/PopPIPE/pull/9

Full Changelog: https://github.com/bacpop/PopPIPE/compare/v1.0.0...v1.1.0

- Python
Published by johnlees about 2 years ago

poppipe - v1.0.0: First pipeline

Use new microreact api, better tree handling with ete3

What's Changed

  • Add helper script for assign runs by @johnlees in https://github.com/bacpop/PopPIPE/pull/3
  • Upgrade to first release by @johnlees in https://github.com/bacpop/PopPIPE/pull/6
  • Add version tags to docker image by @johnlees in https://github.com/bacpop/PopPIPE/pull/7

New Contributors

  • @johnlees made their first contribution in https://github.com/bacpop/PopPIPE/pull/3

Full Changelog: https://github.com/bacpop/PopPIPE/commits/v1.0.0

- Python
Published by johnlees almost 4 years ago