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 #69
• Bumped version by @nikhil in #70
• Release 1.2 by @nikhil in #71

Full Changelog: 1.1.1...1.2.0

1.1.1

What's Changed

• Metadata bug fix for netmhc tools #64
• Fix broken download pipeline test #68
• Update templates to meet the latest nf-core standard #65

Full Changelog: 1.1.0...1.1.1

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 #52
• Added a TSV output that is more easily readable
• Changed how NetMHC tools look for the TMP directory in #55 and #56
• Laid groundwork for SV integration

Full Changelog: 1.0.0...1.1.0

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

New Contributors

• @johnoooh made their first contribution in #32
• @nikhil made their first contribution in #36

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