neoantigen-pipeline - 1.3.1

Features

• NMD edge case fix
• Cleanup modules folder

What's Changed

• BUGFIX: updated generateinput by @johnoooh in https://github.com/mskcc/neoantigen-pipeline/pull/77
• Bump version by @nikhil in https://github.com/mskcc/neoantigen-pipeline/pull/78
• Release 1.3.1 by @nikhil in https://github.com/mskcc/neoantigen-pipeline/pull/79

Full Changelog: https://github.com/mskcc/neoantigen-pipeline/compare/1.3.0...1.3.1

- Python
Published by nikhil about 1 year ago

neoantigen-pipeline - 1.3.0

Features

• Improved documentation
• Added NMD support
• Configure compute fitness weights
• Fixed output file names

What's Changed

• NMD and config fixes by @nikhil and @johnoooh in https://github.com/mskcc/neoantigen-pipeline/pull/74
• Release 1.3.0 by @nikhil in https://github.com/mskcc/neoantigen-pipeline/pull/75
• Release 1.3.0 by @nikhil in https://github.com/mskcc/neoantigen-pipeline/pull/76

Full Changelog: https://github.com/mskcc/neoantigen-pipeline/compare/1.2.0...1.3.0

- Python
Published by nikhil about 1 year ago

neoantigen-pipeline - 1.2.0

Features

• Fix neoantigen input indel bug
• Added flag to control Kd_cutoff
• Several README fixes
• Update nf-core template

What's Changed

• Bug fix for input generation by @nikhil and @johnoooh in https://github.com/mskcc/neoantigen-pipeline/pull/69
• Bumped version by @nikhil in https://github.com/mskcc/neoantigen-pipeline/pull/70
• Release 1.2 by @nikhil in https://github.com/mskcc/neoantigen-pipeline/pull/71

Full Changelog: https://github.com/mskcc/neoantigen-pipeline/compare/1.1.1...1.2.0

- Python
Published by nikhil about 1 year ago

neoantigen-pipeline - 1.1.1

What's Changed

• Metadata bug fix for netmhc tools https://github.com/mskcc/neoantigen-pipeline/pull/64
• Fix broken download pipeline test https://github.com/mskcc/neoantigen-pipeline/pull/68
• Update templates to meet the latest nf-core standard https://github.com/mskcc/neoantigen-pipeline/pull/65

Full Changelog: https://github.com/mskcc/neoantigen-pipeline/compare/1.1.0...1.1.1

- Python
Published by nikhil about 1 year ago

neoantigen-pipeline - 1.1.0

What's Changed

• Added run options for NetMHC versions. Now NetMHC3.4 is the default and NetMHCpan4.1 is available to run as well
• Updated Documentation in https://github.com/mskcc/neoantigen-pipeline/pull/52
• Added a TSV output that is more easily readable
• Changed how NetMHC tools look for the TMP directory in https://github.com/mskcc/neoantigen-pipeline/issues/55 and https://github.com/mskcc/neoantigen-pipeline/pull/56
• Laid groundwork for SV integration

Full Changelog: https://github.com/mskcc/neoantigen-pipeline/compare/1.0.0...1.1.0

- Python
Published by johnoooh over 1 year ago

neoantigen-pipeline - Release 1.0.0

First release of the neoantigen pipeline!

Contains the following steps:

Create phylogenetic trees using PhyloWGS Use netMHCpan-4 to calculate binding affinities Use netMHCpanStab to calculate stability scores Use Luksza et al.'s neoantigen quality and fitness computations tool (NeoantigenEditing) to evaluate peptides

Docs, tests, and portable modules are included as well!

What's Changed

• Subworkflows merge test by @johnoooh in https://github.com/mskcc/neoantigen-pipeline/pull/32
• Input schema changes from nf-core default to new schema by @johnoooh in https://github.com/mskcc/neoantigen-pipeline/pull/33
• Adding netmhcpan by @johnoooh in https://github.com/mskcc/neoantigen-pipeline/pull/34
• Update README.md by @johnoooh in https://github.com/mskcc/neoantigen-pipeline/pull/37
• PR for MVP release! (for real) by @nikhil in https://github.com/mskcc/neoantigen-pipeline/pull/36
• Feature/netmhc refactor by @nikhil in https://github.com/mskcc/neoantigen-pipeline/pull/45
• Update input for test config by @nikhil in https://github.com/mskcc/neoantigen-pipeline/pull/48
• Dev by @nikhil in https://github.com/mskcc/neoantigen-pipeline/pull/49
• Feature/update modules to base develop by @nikhil in https://github.com/mskcc/neoantigen-pipeline/pull/50
• Dev by @nikhil in https://github.com/mskcc/neoantigen-pipeline/pull/51
• Release candidate for 1.0.0 by @nikhil in https://github.com/mskcc/neoantigen-pipeline/pull/46

New Contributors

• @johnoooh made their first contribution in https://github.com/mskcc/neoantigen-pipeline/pull/32
• @nikhil made their first contribution in https://github.com/mskcc/neoantigen-pipeline/pull/36

Full Changelog: https://github.com/mskcc/neoantigen-pipeline/commits/1.0.0

- Python
Published by nikhil over 1 year ago