0.2.3

What's Changed

• Feature/nmd and other fixes by @johnoooh in #188
• Bugfix/neoinput output json name fix by @johnoooh in #192
• pull changes first before creating md file by @huyu335 in #193
• NMD edge case fix by @johnoooh in #197
• Bug fix on identity handling by @nikhil in #202
• Update generateMutFasta.py to handle new hgvs simple code by @nikhil in #204
• Update generateMutFasta.py by @nikhil in #206
• update nf-test gitactions by @buehlere in #212
• Initial commit for module calculate_noise by @mikefeixu in #213
• Revert "Initial commit for module calculate_noise" by @mikefeixu in #214
• Release/0.2.3 by @buehlere in #218

Full Changelog: 0.1.3...0.2.3

0.1.3

What's Changed

• Release/0.1.2 by @buehlere in #156
• Handle identity edge case for Netmhc by @nikhil in #166
• Made bedpe file optional for neoantigeninput by @nikhil in #167
• Fixed netmhc workflow typo by @nikhil in #168
• Update CI and fix Singularity Bug by @buehlere in #174
• Update PULL_REQUEST_TEMPLATE.md by @nikhil in #158
• Bugfix netmhc feature names by @johnoooh in #172
• Hotfix module yaml to markdown issue by @huyu335 in #176
• Bugfix/neoantigen input indel fixes by @johnoooh in #182
• remove meta map from versions output channel by @anoronh4 in #183
• Rewrite to include structure in summary file by @huyu335 in #184
• Updated version in snap file by @nikhil in #187

Full Changelog: 0.1.2...0.1.3

0.1.2

What's Changed

• Release/0.1.1 by @buehlere in #130
• Fix auto linting issue by @huyu335 in #132
• hotfix for documentation by @buehlere in #134
• Hotfix for gitbook sync by @huyu335 in #136
• Feature/neosv by @johnoooh in #124
• Remove 'name' field as mandatory from environment_schema.json by @rnaidu in #143
• Updating Genome Nexus Subworkflow + Modules (for nucleovar nf-core lint check) by @rnaidu in #141
• Mutect1 lint update by @rnaidu in #144
• updating traceback subworkflow with local changes made to pass nf-cor… by @rnaidu in #145
• Update test.yml specifically verify markdown part with new schema associated with modules by @rhshah in #151
• Adding AGPL license by @rhshah in #150
• updated traceback subworkflow and associated modules with changes for… by @rnaidu in #149
• Allow num_chains to be set in the config by @nikhil in #148
• big lint fix by @buehlere in #157
• Develop by @buehlere in #163
• Adding codeowners action by @rhshah in #164
• Update several neoantigen tools by @nikhil in #162
• Update/genome nexus by @buehlere in #165

Full Changelog: 0.1.1...0.1.2

0.1.1

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

Initial Release

• Created inital framework to collaborate using nf-core and Nextflow
• Made Gitbook documentation
• Formalize PR
• Formalize linting
• Add container documentation
• Testing pushing image to Jfrog
• Following modules added:
  • Mutect1
  • Polysolver
  • GBCMS
  • facets
  • snppileup
  • gatk4/applybqsr
  • custom/splitfastqbylane

What's Changed

• Subworkflows/bam generation using nfcore with nextflow initialization by @anoronh4 in #6
• Nf test/gbcms by @buehlere in #10
• Feature/gbcms by @buehlere in #3
• added polysolver modules with nf-test by @anoronh4 in #12
• add gatk4/applybqsr by @anoronh4 in #14
• add custom/splitfastqbylane module by @anoronh4 in #23
• Includes module and tests for mutect1 by @rnaidu in #32
• Feature: add sync meta yml gitbook by @huyu335 in #25
• Module:snppileup by @nikhil in #24
• Update snppileup input description by @nikhil in #45
• Add Facets module by @nikhil in #34
• Feature/prs by @buehlere in #33
• adding new linting schema by @buehlere in #36
• remove bwa_markdup_bqsr subworkflow by @anoronh4 in #62
• Update gitbook sync by @huyu335 in #55

New Contributors

• @anoronh4 made their first contribution in #6
• @buehlere made their first contribution in #10
• @rnaidu made their first contribution in #32
• @huyu335 made their first contribution in #25

Full Changelog: https://github.com/mskcc-omics-workflows/modules/commits/0.1.0