v0.5.1

What's Changed

• Fixed bug with input handling inside docker execution
• Bump conda-incubator/setup-miniconda from 3.0.4 to 3.2.0 by @dependabot[bot] in #80
• Bump actions/upload-artifact from 4 to 6 by @dependabot[bot] in #79
• Bump actions/checkout from 4.1.4 to 6.0.1 by @dependabot[bot] in #78
• Bump actions/setup-java from 4.5.0 to 5.1.0 by @dependabot[bot] in #77
• Bump mikepenz/action-junit-report from 4 to 6 by @dependabot[bot] in #76

Full Changelog: v0.5.0...v0.5.1

v0.5.0

Changes and fixes introduced in v0.5.0:

• renamed input_folder parameter to input. input accepts now also (remote) archive tarball files.
• better configuration setup (close to nf-core)
• improved resource allocation for nextflow
• improved handling of alternative splicing variants in reporting
• adding test profile and nf-test based CI checks

Full Changelog: v0.4.1...v0.5.0

v0.4.0

What's Changed

• Update OrthoXMLSplitter.py by @spascarelli in #33
• Added alternative base config by @ens-sb in #24
• fix: issue #59 by @ali-yz in #60
• Requesting minimum set of config updates for big dataset by @Simarpreet-Kaur-Bhurji in #68
• Improvements for nextflow: alternative version selection, README updates
• Split HOG and sampling improvements
• ensure orthologGroup at the MRCA of all genes in the group
• Docker improvements, additional labels and tools
• New gene families with mmseqs easy-cluster if mmseqs is installed
• Improved input checking
• Merge rootHOGs, improved handling of singleton using omamer multi-hits
• Various documentation and usability updates

New Contributors

• @spascarelli made their first contribution in #33
• @ali-yz made their first contribution in #60
• @Simarpreet-Kaur-Bhurji made their first contribution in #68

Full Changelog: v0.3.5...v0.4.0

v0.3.4

Full Changelog: v0.3.3...v0.3.4

v0.3.2

Full Changelog: v0.3.1...v0.3.2

v0.2.0

What's Changed

• Improved pipeline
• Added automatically generated report based on jupyter notebook
• Bump actions/setup-python from 4 to 5 by @dependabot in #10
• Bump docker/metadata-action from 4 to 5 by @dependabot in #11
• Bump actions/checkout from 3 to 4 by @dependabot in #17
• Bump pypa/gh-action-pypi-publish from 1.4.2 to 1.8.11 by @dependabot in #16
• Bump docker/login-action from 2 to 3 by @dependabot in #15

New Contributors

• @dependabot made their first contribution in #10

Full Changelog: v0.1.6...v0.2.0

v0.1.6

What's Changed

• update nf and roothogMering by @sinamajidian in #9

Full Changelog: v0.1.4...v0.1.6

Release v0.1.4

• Find new gene families with linclust if mmseqs is installed
• use quoted protein name to handle special chars in fasta record
• check input first

Release v0.1.3

Update FastOMA.nf

Release v0.1.0

Release v0.1.0: improved nextflow pipeline with OGs as outputs. 3 Sep. 2023.