covpipe2 - Version v0.5.2

What's Changed

• Marie lataretu/issue72 by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/74
  • fixed #71 and #72
  • thanks to @anfarr and @hoelzer

Full Changelog: https://github.com/rki-mf1/CoVpipe2/compare/v0.5.1...v0.5.2

- Nextflow
Published by MarieLataretu almost 2 years ago

covpipe2 - Version v0.5.1

What's Changed

• added parameters seqthreshold and nthreshold by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/70

Full Changelog: https://github.com/rki-mf1/CoVpipe2/compare/v0.5.0...v0.5.1

- Nextflow
Published by MarieLataretu almost 2 years ago

covpipe2 - Version v0.5.0

What's Changed

• added -r to nextflow run repo/tool calls by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/67
• Update nextclade3 by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/68
• Release v0.5 by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/69

Full Changelog: https://github.com/rki-mf1/CoVpipe2/compare/v0.4.3...v0.5.0

- Nextflow
Published by MarieLataretu almost 2 years ago

covpipe2 - Version v0.4.3

What's Changed

• changed channel order for conda envs by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/63
• fixed reporting on the nextclade dataset tag by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/64

Full Changelog: https://github.com/rki-mf1/CoVpipe2/compare/v0.4.1...v0.4.3

- Nextflow
Published by MarieLataretu over 2 years ago

covpipe2 - Version v0.4.2

• added a Digital Object Identifiers (DOI) on Zenodo

- Nextflow
Published by MarieLataretu over 2 years ago

covpipe2 - Version v0.4.1

What's Changed

• Add citations by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/61
• added badges by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/62

Full Changelog: https://github.com/rki-mf1/CoVpipe2/compare/v0.4.0...v0.4.1

- Nextflow
Published by MarieLataretu almost 3 years ago

covpipe2 - Version v0.4.0

What's Changed

• exchanged deprecated implicit variable by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/55
• conda directive correctly set in standard profile by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/57
• Enhancment nextclade dataset version by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/58
• Feature filter indels by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/59
• v0.4.0 by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/60

Full Changelog: https://github.com/rki-mf1/CoVpipe2/compare/v0.3.4...v0.4.0

- Nextflow
Published by MarieLataretu almost 3 years ago

covpipe2 - Version v0.3.4

What's Changed

• Fix report summary header by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/54
• updated default pangolin version to 4.2 with data version 1.18.1.1
• updated default nextclade@2.13.1

Full Changelog: https://github.com/rki-mf1/CoVpipe2/compare/v0.3.3...v0.3.4

- Nextflow
Published by MarieLataretu almost 3 years ago

covpipe2 - Version v0.3.3

What's Changed

• correct md5sums for latest nextclade and pangolin versions by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/52
• [enhancement] timestamp in report by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/53

Full Changelog: https://github.com/rki-mf1/CoVpipe2/compare/v0.3.2...v0.3.3

- Nextflow
Published by MarieLataretu almost 3 years ago

covpipe2 - Version v0.3.2

What's Changed

• added conda.enabled = true to config by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/50

Full Changelog: https://github.com/rki-mf1/CoVpipe2/compare/v0.3.1...v0.3.2

- Nextflow
Published by MarieLataretu about 3 years ago

covpipe2 - Version v0.3.1

What's Changed

• Create LICENSE.md by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/47
• use sc2rf from ncov-recombinant repo by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/48

Full Changelog: https://github.com/rki-mf1/CoVpipe2/compare/v0.3.0...v0.3.1

- Nextflow
Published by MarieLataretu about 3 years ago

covpipe2 - Version v0.3.0

What's Changed

• Version v0.3 by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/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: https://github.com/rki-mf1/CoVpipe2/compare/v0.2.9...v0.3.0

- Nextflow
Published by MarieLataretu about 3 years ago

covpipe2 - Version v0.2.9

What's Changed

• [Feature] full single end support by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/45

Full Changelog: https://github.com/rki-mf1/CoVpipe2/compare/v0.2.8...v0.2.9

- Nextflow
Published by MarieLataretu over 3 years ago

covpipe2 - Version v0.2.8

What's Changed

• fixed https://github.com/rki-mf1/CoVpipe2/issues/43
• added additional params for bamclipper
• fixed rki report output
• added inset size filter option
• added pangolin-data to pang env/container

Full Changelog: https://github.com/rki-mf1/CoVpipe2/compare/v0.2.7...v0.2.8

- Nextflow
Published by MarieLataretu over 3 years ago

covpipe2 - 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: https://github.com/rki-mf1/CoVpipe2/compare/v0.2.6...v0.2.7

- Nextflow
Published by MarieLataretu over 3 years ago

covpipe2 - Version v0.2.6

Fixed

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

Full Changelog: https://github.com/rki-mf1/CoVpipe2/compare/v0.2.5...v0.2.6

- Nextflow
Published by MarieLataretu over 3 years ago

covpipe2 - Version v0.2.5

What's Changed

• MarieLataretu/issue39 by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/40
• MarieLataretu/issue39 by @MarieLataretu

Full Changelog: https://github.com/rki-mf1/CoVpipe2/compare/v0.2.4...v0.2.5

- Nextflow
Published by MarieLataretu over 3 years ago

covpipe2 - Version v0.2.4

What's Changed

• MarieLataretu/issue34 by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/35
• [FEATURE] added sc2rf by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/36
• Release v0.2.4 by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/37

Full Changelog: https://github.com/rki-mf1/CoVpipe2/compare/v0.2.3...v0.2.4

- Nextflow
Published by MarieLataretu over 3 years ago

covpipe2 - Version v0.2.3

What's Changed

• Dev by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/33
  • simplifies/removes deletion related process for variant calling
  • hotfix for container execution for pangolin and nextclade
  • fixes #31
  • fixes #32

Full Changelog: https://github.com/rki-mf1/CoVpipe2/compare/v0.2.2...v0.2.3

- Nextflow
Published by MarieLataretu over 3 years ago

covpipe2 - Version v0.2.2

What's Changed

• make conda update more stable by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/28
• Hotfix to disable var_sap by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/30
• Simplify deletion handling at consensus generation by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/30

Full Changelog: https://github.com/rki-mf1/CoVpipe2/compare/v0.2.1...v0.2.2

- Nextflow
Published by MarieLataretu over 3 years ago

covpipe2 - Version v0.2.1

What's Changed

• LCS updates: Dev by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/26

Full Changelog: https://github.com/rki-mf1/CoVpipe2/compare/v0.2.0...v0.2.1

- Nextflow
Published by MarieLataretu almost 4 years ago

covpipe2 - Version v0.2.0

What's Changed

• subtract instead of merge by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/22
• Marie lataretu/issue1 by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/23
• Dev by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/25

Full Changelog: https://github.com/rki-mf1/CoVpipe2/compare/v0.1.2...v0.2.0

- Nextflow
Published by MarieLataretu almost 4 years ago

covpipe2 - Version v0.1.2

What's Changed

• Dev by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/21

Full Changelog: https://github.com/rki-mf1/CoVpipe2/compare/v0.1.1...v0.1.2

- Nextflow
Published by MarieLataretu almost 4 years ago

covpipe2 - Version v0.1.1

What's Changed

• krona fails with mamba/conda execution #10 by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/14
• fixes pangolin update #15 by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/17
• update nextclade #16 by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/18

Full Changelog: https://github.com/rki-mf1/CoVpipe2/compare/v0.1.1-alpha...v0.1.0

- Nextflow
Published by MarieLataretu almost 4 years ago

covpipe2 - Version v0.1.1-alpha

What's Changed

• DESH support by @MarieLataretu in https://github.com/rki-mf1/CoVpipe2/pull/13

Full Changelog: https://github.com/rki-mf1/CoVpipe2/compare/v0.1.0-alpha...v0.1.1-alpha

- Nextflow
Published by MarieLataretu almost 4 years ago

covpipe2 - Version v0.1.0-alpha

First (pre-)release on GitHub 🥳

- Nextflow
Published by MarieLataretu almost 4 years ago