Version v0.3.1

What's Changed

• Create LICENSE.md by @MarieLataretu in #47
• use sc2rf from ncov-recombinant repo by @MarieLataretu in #48

Full Changelog: v0.3.0...v0.3.1

Version v0.3.0

What's Changed

• Version v0.3 by @MarieLataretu in #46
  • fixed typos
  • added test profile
  • sc2rf output handling more robust
  • default reference now sars-cov-2
  • report fix (in case of many samples)
  • corrected file extension
  • CI end-to-end test

Full Changelog: v0.2.9...v0.3.0

Version v0.2.9

What's Changed

• [Feature] full single end support by @MarieLataretu in #45

Full Changelog: v0.2.8...v0.2.9

Version v0.2.8

What's Changed

• fixed #43
• added additional params for bamclipper
• fixed rki report output
• added inset size filter option
• added pangolin-data to pang env/container

Full Changelog: v0.2.7...v0.2.8

Version v0.2.7

What's Changed

Fixed

• fixed Nextclade2 Docker auto-update

Changed

• updated Nextclade to version 2: CoVpipe2 not compatible with nextclade version < 2.4.0
• updated Pangolin to version 4.1.2

Removed

• parameter pangolin_scorpio, since pangolin default behaviour changed from v4.1

Full Changelog: v0.2.6...v0.2.7

Version v0.2.6

Fixed

• report can handle Kraken2 output with no human, unclassified or tax_id reads

Full Changelog: v0.2.5...v0.2.6

Version v0.2.5

What's Changed

• MarieLataretu/issue39 by @MarieLataretu in #40
• MarieLataretu/issue39 by @MarieLataretu

Full Changelog: v0.2.4...v0.2.5

Version v0.2.4

What's Changed

• MarieLataretu/issue34 by @MarieLataretu in #35
• [FEATURE] added sc2rf by @MarieLataretu in #36
• Release v0.2.4 by @MarieLataretu in #37

Full Changelog: v0.2.3...v0.2.4

Version v0.2.3

What's Changed

• Dev by @MarieLataretu in #33
  • simplifies/removes deletion related process for variant calling
  • hotfix for container execution for pangolin and nextclade
  • fixes #31
  • fixes #32

Full Changelog: v0.2.2...v0.2.3

Version v0.2.2

What's Changed

• make conda update more stable by @MarieLataretu in #28
• Hotfix to disable var_sap by @MarieLataretu in #30
• Simplify deletion handling at consensus generation by @MarieLataretu in #30

Full Changelog: v0.2.1...v0.2.2