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Release candidate for 1.0.0 #46

Merged
merged 134 commits into from
Jul 31, 2024
Merged

Release candidate for 1.0.0 #46

merged 134 commits into from
Jul 31, 2024

Commits on Mar 20, 2024

  1. Install modules from mskcc-omics repo

    @nikhil
    nikhil committed Mar 20, 2024
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  2. Add references to main pipeline

    @nikhil
    nikhil committed Mar 20, 2024
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Commits on Mar 25, 2024

  1. Changed README description, input samplesheet 

    preparing for subworkflow inclusion
    @johnoooh
    johnoooh committed Mar 25, 2024
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Commits on Apr 1, 2024

  1. Added new subworkflows, updated modules, added netmhcstabpan

    @johnoooh
    johnoooh committed Apr 1, 2024
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  2. changed from capital to lowercase

    @johnoooh
    johnoooh committed Apr 1, 2024
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  3. iedb moved test

    @johnoooh
    johnoooh committed Apr 1, 2024
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  4. computeFitness -> computefitness

    @johnoooh
    johnoooh committed Apr 1, 2024
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  5. Merge pull request #32 from mskcc/subworkflows 

    Subworkflows merge test
    @nikhil
    nikhil authored Apr 1, 2024
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Commits on Apr 2, 2024

  1. Update schema_input.json

    @johnoooh
    johnoooh committed Apr 2, 2024
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  2. Update README.md

    @johnoooh
    johnoooh authored Apr 2, 2024
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  3. Update samplesheet.csv

    @johnoooh
    johnoooh authored Apr 2, 2024
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  4. Update schema_input.json 

    tempo_maf -> maf for clarity
    @johnoooh
    johnoooh authored Apr 2, 2024
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  5. Merge pull request #33 from mskcc/inputschema 

    Input schema changes from nf-core default to new schema
    @nikhil
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  6. Adding netmhcpan 

    netmhcstabpan still in development
    @johnoooh
    johnoooh committed Apr 2, 2024
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  7. Merge pull request #34 from mskcc/feature/netmhcpan 

    Adding netmhcpan
    @nikhil
    nikhil authored Apr 2, 2024
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Commits on Apr 3, 2024

  1. test profile added, running currently 

    nf-test added but not yet working.  Neoantigen pipeline almost assembled.  Just need to add neoantigenediting.

Lots more to do
    @johnoooh
    johnoooh committed Apr 3, 2024
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  2. Multievolve chain reduction

    @johnoooh
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Commits on Apr 4, 2024

  1. Ignore .nf-test.log

    @nikhil
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Commits on Apr 5, 2024

  1. Pipeline workign with some changes to modules 

    Changes incoming
    @johnoooh
    johnoooh committed Apr 5, 2024
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Commits on Apr 8, 2024

  1. Module fixes

    @johnoooh
    johnoooh committed Apr 8, 2024
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  2. neoantigen input update

    @johnoooh
    johnoooh committed Apr 8, 2024
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Commits on Apr 9, 2024

  1. Neoantigenediting

    @johnoooh
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  2. netmhcpan test update

    @johnoooh
    johnoooh committed Apr 9, 2024
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  3. Set process to medium

    @nikhil
    nikhil committed Apr 9, 2024
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  4. Update neoantigeninput

    @nikhil
    nikhil committed Apr 9, 2024
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  5. Some cleanup

    @nikhil
    nikhil committed Apr 9, 2024
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  6. Add github action

    @nikhil
    nikhil committed Apr 9, 2024
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  7. Update test config to have relative path

    @nikhil
    nikhil committed Apr 9, 2024
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  8. Add github action

    @nikhil
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  9. Update README.md 

    Added workflow steps to introduction.
    @johnoooh
    johnoooh authored Apr 9, 2024
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  10. Merge pull request #37 from mskcc/workflow_steps 

    Update README.md
    @nikhil
    nikhil authored Apr 9, 2024
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  11. Change emit channel for pipeline 

    emit channel was still placeholder.  Should be good now.
    @johnoooh
    johnoooh authored Apr 9, 2024
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  12. Fix neo_out

    @johnoooh
    johnoooh authored Apr 9, 2024
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  13. Update main.nf 

    Updated to change neoin to neo_out to go along with previous commit
    @johnoooh
    johnoooh authored Apr 9, 2024
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  14. Prettier and linted

    @johnoooh
    johnoooh committed Apr 9, 2024
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  15. Updated netmhcpan remote module

    @nikhil
    nikhil committed Apr 9, 2024
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Commits on Apr 10, 2024

  1. Fix linting

    @nikhil
    nikhil committed Apr 10, 2024
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  2. More linting fixes

    @nikhil
    nikhil committed Apr 10, 2024
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  3. Make README prettier

    @nikhil
    nikhil committed Apr 10, 2024
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  4. Update modules

    @nikhil
    nikhil committed Apr 10, 2024
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  5. Update README

    @nikhil
    nikhil committed Apr 10, 2024
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  6. README linting

    @nikhil
    nikhil committed Apr 10, 2024
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  7. Ignore README linting, the formatting of a markdown doc does not matter

    @nikhil
    nikhil committed Apr 10, 2024
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  8. Add readme extension

    @nikhil
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  9. Merge branch 'dev' of github.com:mskcc/NeoAntigen-Pipeline into test_… 

    …profile_run
    @nikhil
    nikhil committed Apr 10, 2024
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  10. Lets not go overboard on linting

    @nikhil
    nikhil committed Apr 10, 2024
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  11. Update neoantigeninput module

    @nikhil
    nikhil committed Apr 10, 2024
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  12. Merge pull request #36 from mskcc/test_profile_run 

    PR for MVP release! (for real)
    @johnoooh
    johnoooh authored Apr 10, 2024
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Commits on Jun 7, 2024

  1. Added new modules for netmhcpan processing refactor

    @nikhil
    nikhil committed Jun 7, 2024
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  2. Updated nf-core subworkflow

    @nikhil
    nikhil committed Jun 7, 2024
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  3. Updated workflow to work with netmhcpan refactor

    @nikhil
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Commits on Jun 8, 2024

  1. Updated file for testing

    @nikhil
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Commits on Jun 13, 2024

  1. Added production config

    @nikhil
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  2. Updated nextflow modules

    @nikhil
    nikhil committed Jun 13, 2024
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  3. Update facets line to use the hisens instead of genelevel.

    @nikhil
    nikhil committed Jun 13, 2024
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  4. Merge branch 'feature/netmhc_refactor' of github.com:mskcc/NeoAntigen… 

    …-Pipeline into feature/netmhc_refactor
    @nikhil
    nikhil committed Jun 13, 2024
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  5. Linting fixes

    @nikhil
    nikhil committed Jun 13, 2024
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  6. Formatting fix

    @nikhil
    nikhil committed Jun 13, 2024
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  7. Automatic fix for files_unchanged linting errors

    @nikhil
    nikhil committed Jun 13, 2024
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  8. Removed unused processes in the modules config

    @nikhil
    nikhil committed Jun 13, 2024
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  9. Removed unused module

    @nikhil
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  10. Unset editorconfig for msk modules and subworkflows

    @nikhil
    nikhil committed Jun 13, 2024
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  11. Removed zenodo cite

    @nikhil
    nikhil committed Jun 13, 2024
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  12. Removed empty zenodo link

    @nikhil
    nikhil committed Jun 13, 2024
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  13. Set nf-core version

    @nikhil
    nikhil committed Jun 13, 2024
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Commits on Jun 14, 2024

  1. Update download_pipeline.yml

    @nikhil
    nikhil authored Jun 14, 2024
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  2. revert nf-core tools downgrade

    @nikhil
    nikhil authored Jun 14, 2024
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  3. Add phylowgs config for test and prod

    @nikhil
    nikhil committed Jun 14, 2024
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  4. Disable pipeline download test

    @nikhil
    nikhil committed Jun 14, 2024
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  5. Merge branch 'feature/netmhc_refactor' of github.com:mskcc/NeoAntigen… 

    …-Pipeline into feature/netmhc_refactor
    @nikhil
    nikhil committed Jun 14, 2024
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Commits on Jun 17, 2024

  1. Update modules and subworkflows

    @nikhil
    nikhil committed Jun 17, 2024
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  2. Corrected facets samplesheet header

    @nikhil
    nikhil committed Jun 17, 2024
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  3. Slight fix in schema input rename

    @nikhil
    nikhil committed Jun 17, 2024
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  4. Made schema input prettier

    @nikhil
    nikhil committed Jun 17, 2024
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Commits on Jun 20, 2024

  1. Made schema input prettier

    @nikhil
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  2. Update modules and subworkflows

    @nikhil
    nikhil committed Jun 20, 2024
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  3. Default to a long walltime for phylowgs

    @nikhil
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  4. Outout results per sample

    @nikhil
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  5. Allow multiprimary samples from phylowgs

    @nikhil
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  6. Conf to run with lsf and singularity

    @nikhil
    nikhil committed Jun 20, 2024
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  7. Set appropriate max limits

    @nikhil
    nikhil committed Jun 20, 2024
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  8. Merge branch 'feature/netmhc_refactor' of github.com:mskcc/NeoAntigen… 

    …-Pipeline into feature/netmhc_refactor
    @nikhil
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Commits on Jun 21, 2024

  1. Add missing data folder for computefitness

    @nikhil
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Commits on Jul 2, 2024

  1. Update modules

    @nikhil
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  2. Some cleanup

    @nikhil
    nikhil committed Jul 2, 2024
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  3. Remove artifacts

    @nikhil
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Commits on Jul 3, 2024

  1. Update README

    @nikhil
    nikhil committed Jul 3, 2024
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  2. Add workflow diagram image

    @nikhil
    nikhil committed Jul 3, 2024
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  3. Made README prettier

    @nikhil
    nikhil committed Jul 3, 2024
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  4. Made citations prettier

    @nikhil
    nikhil committed Jul 3, 2024
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  5. Made modules prettier

    @nikhil
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  6. Add updated README

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  7. Update linting and tests

    @nikhil
    nikhil committed Jul 3, 2024
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  8. Add workflow image

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  9. Fix modules json

    @nikhil
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  10. Updated modules json

    @nikhil
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  11. Add black formatting

    @nikhil
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  12. Add black formatted file

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  13. Fix linting

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Commits on Jul 5, 2024

  1. Removed unused config parameter

    @nikhil
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  2. Removed unused config parameter (part 2)

    @nikhil
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  3. Update nextflow.config

    @nikhil
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  4. Cleanup prod.config

    @nikhil
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  5. Removed unused parameter from modules.config

    @nikhil
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  6. Cleaned up test.config

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Commits on Jul 8, 2024

  1. Merge pull request #45 from mskcc/feature/netmhc_refactor 

    Feature/netmhc refactor
    @nikhil
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  2. Update output.md 

    Almost done with output
    @johnoooh
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  3. Update output.md

    @johnoooh
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  4. Adding picture, removing old fastqc pics

    @johnoooh
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Commits on Jul 18, 2024

  1. update parse cnvs

    John Orgera committed Jul 18, 2024
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Commits on Jul 29, 2024

  1. Made code prettier 🌸

    @nikhil
    nikhil committed Jul 29, 2024
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  2. Removed unused modules

    @nikhil
    nikhil committed Jul 29, 2024
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  3. Made code prettier (again) 🌷

    @nikhil
    nikhil committed Jul 29, 2024
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  4. Update modules json

    @nikhil
    nikhil committed Jul 29, 2024
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  5. Re-enable download_pipeline.yml

    @nikhil
    nikhil authored Jul 29, 2024
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  6. Set relative path to samplesheet

    @nikhil
    nikhil authored Jul 29, 2024
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  7. Use double quotes instead

    @nikhil
    nikhil authored Jul 29, 2024
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  8. Update input for test config

    @nikhil
    nikhil authored Jul 29, 2024
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  9. Update test.config

    @nikhil
    nikhil authored Jul 29, 2024
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Commits on Jul 30, 2024

  1. Merge pull request #48 from mskcc/feature/update_input_samplesheet_path 

    Update input for test config
    @johnoooh
    johnoooh authored Jul 30, 2024
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  2. Merge pull request #49 from mskcc/dev 

    Update pipeline download test
    @nikhil
    nikhil authored Jul 30, 2024
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  3. Update to use modules from develop

    @nikhil
    nikhil committed Jul 30, 2024
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  4. Cleanup EpitopeDistance.py

    @nikhil
    nikhil authored Jul 30, 2024
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  5. Merge pull request #50 from mskcc/feature/update_modules_to_base_develop 

    Feature/update modules to base develop
    @nikhil
    nikhil authored Jul 30, 2024
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  6. Merge pull request #51 from mskcc/dev 

    Dev
    @nikhil
    nikhil authored Jul 30, 2024
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  7. Add master PR for ci tessts

    @nikhil
    nikhil authored Jul 30, 2024
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  8. Add master PR for ci tests

    @nikhil
    nikhil committed Jul 30, 2024
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  9. Merge branch 'release/candidate-1.0.0' of github.com:mskcc/NeoAntigen… 

    …-Pipeline into release/candidate-1.0.0
    @nikhil
    nikhil committed Jul 30, 2024
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Commits on Jul 31, 2024

  1. Update usage.md 

    edited usage doc
    @johnoooh
    johnoooh authored Jul 31, 2024
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  2. Update usage.md

    @johnoooh
    johnoooh authored Jul 31, 2024
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  3. Update .editorconfig

    @johnoooh
    johnoooh authored Jul 31, 2024
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  4. Update usage.md

    @johnoooh
    johnoooh authored Jul 31, 2024
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  5. Update .editorconfig

    @johnoooh
    johnoooh authored Jul 31, 2024
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  6. Made docs code prettier

    @nikhil
    nikhil committed Jul 31, 2024
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