What's Changed
- Add neoantigen branch to ci tests by @nikhil in #49
- Module phylowgs parser by @pintoa1-mskcc in #48
- Module: phylowgs create inputs by @pintoa1-mskcc in #51
- Organize phylowgs tool level modules by @nikhil in #52
- Add phylowgs writeresults by @nikhil in #54
- Add phylowgs multievolve by @nikhil in #53
- Ignore conda test for netmhcpan by @nikhil in #59
- New Module: Neoantigen inputs by @johnoooh in #57
- Netmhcpan Pull by @johnoooh in #56
- Add module neoantigenediting alignto iedb by @nikhil in #60
- Feature/add module neoantigenediting computefitness by @nikhil in #61
- Some updates and minor fixes to tests and formatting for various neoantigen modules by @nikhil in #70
- Add phylowgs subworkflow by @nikhil in #73
- neoantigenEditing subworkflow by @johnoooh in #63
- Fix module linting by @nikhil in #74
- Feature/netmhcstabpan by @johnoooh in #76
- Hotfix/verify md by @huyu335 in #77
- Feature/netmhcpan optimize by @johnoooh in #79
- hotfix/neoantigeninput - changing inputs by @johnoooh in #80
- Hotfix/neoantigeninputs version by @johnoooh in #81
- Fix neoantigen editing subworkflow by @nikhil in #82
- Add all the linting by @nikhil in #83
- Handle single layer zip structure by @nikhil in #84
- Fix/pytest yml by @buehlere in #90
- add .editorconfig file by @anoronh4 in #88
- Feature/netmhcstabpan by @johnoooh in #85
- Merge with dev by @nikhil in #91
- Feature/netmhc refactor by @nikhil in #93
- Feature/id addition by @johnoooh in #96
- Update phylowgs to a new version that can parse facets hisens.cncf by @nikhil in #95
- Fix generate_input id bug by @nikhil in #97
- Just some cleanup of print statements by @nikhil in #98
- Add arg for writeresults by @nikhil in #99
- handle NA values for cellularity by @nikhil in #100
- Update version of neoantigenediting tools by @nikhil in #101
- Feature/indel assigning by @johnoooh in #104
- Set phylowgs chains to thread count by @nikhil in #105
- Feature/add rediscoverte by @nikhil in #103
- Update tags by @nikhil in #106
- Renamed data folder as data is in other gitignores by @nikhil in #107
- Fix cellularity logic for facets input by @nikhil in #108
- Subworkflow: genome nexus - vcf2maf + annotationpipeline by @rnaidu in #58
- Adding README by @rhshah in #94
- Feature/add neoantigen modules by @nikhil in #110
- Small fixes for rediscoverte by @nikhil in #115
- Subworkflow:traceback by @buehlere in #47
- changed versioning of annotation pipeline module in genome nexus subw… by @rnaidu in #118
- Update java vm args by @nikhil in #121
- Module:ppflagfixer by @huyu335 in #43
- Fix stub test for formatnetmhcpan by @nikhil in #123
- Feature/neo tsv by @johnoooh in #117
- Hotfix/update test dataset links by @huyu335 in #92
- fixing PR template by @buehlere in #128
- Update test bam locations by @huyu335 in #131
New Contributors
- @pintoa1-mskcc made their first contribution in #48
- @johnoooh made their first contribution in #57
- @rhshah made their first contribution in #94
Full Changelog: 0.1.0...0.1.1