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Release/0.1.1 #130

Merged
merged 552 commits into from
Aug 28, 2024
Merged

Release/0.1.1 #130

merged 552 commits into from
Aug 28, 2024
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Apr 18, 2024

  1. Merge branch 'develop' into fix/pytest_yml

    @buehlere
    buehlere authored Apr 18, 2024
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Commits on Apr 19, 2024

  1. Merge pull request #90 from mskcc-omics-workflows/fix/pytest_yml 

    Fix/pytest yml
    @buehlere
    buehlere authored Apr 19, 2024
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  2. fix editorconfig linting errors

    Anne Marie Noronha committed Apr 19, 2024
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  3. fix snapshot

    Anne Marie Noronha committed Apr 19, 2024
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  4. fix snapshot

    Anne Marie Noronha committed Apr 19, 2024
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Commits on Apr 22, 2024

  1. Merge branch 'develop' into update/editorconfig_config

    @anoronh4
    anoronh4 authored Apr 22, 2024
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Commits on Apr 23, 2024

  1. Merge pull request #88 from mskcc-omics-workflows/update/editorconfig… 

    …_config

add .editorconfig file
    @anoronh4
    anoronh4 authored Apr 23, 2024
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Commits on Apr 24, 2024

  1. Merge branch 'develop' of github.com:mskcc-omics-workflows/modules in… 

    …to neoantigen
    @nikhil
    nikhil committed Apr 24, 2024
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  2. Merge branch 'neoantigen' into feature/netMHCstabpan

    @nikhil
    nikhil authored Apr 24, 2024
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  3. Merge pull request #85 from mskcc-omics-workflows/feature/netMHCstabpan 

    Feature/netmhcstabpan
    @nikhil
    nikhil authored Apr 24, 2024
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  4. Merge branch 'neoantigen' of github.com:mskcc-omics-workflows/modules… 

    … into feature/merge_with_dev
    @nikhil
    nikhil committed Apr 24, 2024
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  5. Remove trailing whitespace

    @nikhil
    nikhil committed Apr 24, 2024
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  6. Merge pull request #91 from mskcc-omics-workflows/feature/merge_with_dev 

    Merge with dev
    @nikhil
    nikhil authored Apr 24, 2024
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  7. Merge branch 'develop' into feature/ppflagfixer

    @huyu335
    huyu335 authored Apr 24, 2024
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Commits on May 2, 2024

  1. Remove empty line

    @huyu335
    huyu335 authored May 2, 2024
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  2. Update test data mskcc

    @huyu335
    huyu335 committed May 2, 2024
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  3. update test datasets

    @huyu335
    huyu335 committed May 2, 2024
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Commits on May 6, 2024

  1. Moved neoantigeninput to neoantigenutils

    @nikhil
    nikhil committed May 6, 2024
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  2. Refactor netmhcpan

    @nikhil
    nikhil committed May 6, 2024
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  3. Refactore netmhcstabpan

    @nikhil
    nikhil committed May 6, 2024
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  4. Updated test data

    @nikhil
    nikhil committed May 6, 2024
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  5. Add formatnetmhcpan neoantigenutils module

    @nikhil
    nikhil committed May 6, 2024
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  6. Add generatehlastring neoantigenutils module

    @nikhil
    nikhil committed May 6, 2024
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  7. Add generatemutfasta neoantigenutils module

    @nikhil
    nikhil committed May 6, 2024
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  8. Add netmhcstabandpan subworkflow

    @nikhil
    nikhil committed May 6, 2024
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  9. Fix ECLint

    @nikhil
    nikhil committed May 6, 2024
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  10. Add conda skips

    @nikhil
    nikhil committed May 6, 2024
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  11. Fix meta yml documentation links

    @nikhil
    nikhil committed May 6, 2024
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  12. Ignore conda test for subworkflow

    @nikhil
    nikhil committed May 6, 2024
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  13. Fix name for linting

    @nikhil
    nikhil committed May 6, 2024
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  14. Set ociautopull to help with sif creation

    @nikhil
    nikhil committed May 6, 2024
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  15. Some format fixes

    @nikhil
    nikhil committed May 6, 2024
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  16. Disable autopull

    @nikhil
    nikhil committed May 6, 2024
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Commits on May 7, 2024

  1. Disable singularity test for subworkflow as nextflow hits parallel pull 

    issues
    @nikhil
    nikhil committed May 7, 2024
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  2. Add singularity test back

    @nikhil
    nikhil committed May 7, 2024
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  3. Set netmhctools to the same image to prevent parallel download error

    @nikhil
    nikhil committed May 7, 2024
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  4. fixed typo 

    fixed documentation typo
    @johnoooh
    johnoooh authored May 7, 2024
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Commits on May 8, 2024

  1. Update generateMutFasta.py 

    removed test line
    @johnoooh
    johnoooh authored May 8, 2024
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Commits on May 9, 2024

  1. Merge pull request #93 from mskcc-omics-workflows/feature/netmhc_refa… 

    …ctor

Feature/netmhc refactor
    @johnoooh
    johnoooh authored May 9, 2024
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Commits on May 13, 2024

  1. replaced vcf2maf with vcf2maflite in MSK-module

    @rnaidu
    rnaidu committed May 13, 2024
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  2. resolving trailing whitespace errors

    @rnaidu
    rnaidu committed May 13, 2024
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  3. uploading updated snapshot to pass tests

    @rnaidu
    rnaidu committed May 13, 2024
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  4. uploading updated snapshot to pass tests

    @rnaidu
    rnaidu committed May 13, 2024
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  5. fixing trailspace errors

    @rnaidu
    rnaidu committed May 13, 2024
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Commits on May 24, 2024

  1. Update generateMutFasta.py

    @johnoooh
    johnoooh committed May 24, 2024
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Commits on May 30, 2024

  1. Merge branch 'develop' into traceback

    buehlere committed May 30, 2024
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  2. update image pv maf concat

    buehlere committed May 30, 2024
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  3. removing header as required parameter 

    This should be passed as an optional argument.
    buehlere committed May 30, 2024
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  4. Merge branch 'traceback' into Subworkflow-traceback

    buehlere committed May 30, 2024
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  5. lint updates

    buehlere committed May 30, 2024
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  6. Adding README

    @rhshah
    rhshah committed May 30, 2024
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  7. Update README.md

    @rhshah
    rhshah committed May 30, 2024
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  8. Update README.md

    @rhshah
    rhshah committed May 30, 2024
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Commits on Jun 3, 2024

  1. Update main.nf

    buehlere committed Jun 3, 2024
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Commits on Jun 6, 2024

  1. changed code in main.nf to read in input MAF file as an isolated file… 

    … and not joined with the metamap when being prepared as channel input for the genotype_variants module
    @rnaidu
    rnaidu committed Jun 6, 2024
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  2. removing trailing whitespace to pass github action checks

    @rnaidu
    rnaidu committed Jun 6, 2024
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  3. resolving intermittent HTTP error for conda singularity test

    @rnaidu
    rnaidu committed Jun 6, 2024
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  4. merged annotation pipeline module branch into the final genome nexus … 

    …branch. subworkflow will be built off of here
    @rnaidu
    rnaidu committed Jun 6, 2024
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  5. Update generate_input.py

    @johnoooh
    johnoooh committed Jun 6, 2024
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  6. Merge branch 'feature/genome_nexus_final' of https://github.com/mskcc… 

    …-omics-workflows/modules into feature/genome_nexus_final

fetching recent work pushed to this branch
    @rnaidu
    rnaidu committed Jun 6, 2024
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  7. Merge branch 'feature/genome_nexus_final' of https://github.com/mskcc… 

    …-omics-workflows/modules into feature/genome_nexus_final

pulling recent commits from feature/genome_nexus_final
    @rnaidu
    rnaidu committed Jun 6, 2024
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  8. created genome nexus subworkflow locally and pushing to branch

    @rnaidu
    rnaidu committed Jun 6, 2024
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  9. Merge branch 'feature/genome_nexus_final' of https://github.com/mskcc… 

    …-omics-workflows/modules into feature/genome_nexus_final

pulling recent commits from feature/genome_nexus_final branch into local working branch
    @rnaidu
    rnaidu committed Jun 6, 2024
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  10. adding tested annotation pipeline module for genome nexus subworkflow

    @rnaidu
    rnaidu committed Jun 6, 2024
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  11. passing editor config and prettier checks

    @rnaidu
    rnaidu committed Jun 6, 2024
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  12. passing markdown and linting checks

    @rnaidu
    rnaidu committed Jun 6, 2024
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  13. fixing prettier check

    @rnaidu
    rnaidu committed Jun 6, 2024
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Commits on Jun 10, 2024

  1. Changes to test files and adding another character to the ID

    @johnoooh
    johnoooh committed Jun 10, 2024
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  2. Updating sorting

    @johnoooh
    johnoooh committed Jun 10, 2024
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Commits on Jun 11, 2024

  1. ID done, matching in progress

    @johnoooh
    johnoooh committed Jun 11, 2024
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  2. Updating so SNVS only work and fixing tests 

    Maybe ready to be merge?  I may branch off this to continue to add indel capabilities
    @johnoooh
    johnoooh committed Jun 11, 2024
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  3. Update phylowgs to a new version that can parse facets hisens.cncf

    @nikhil
    nikhil committed Jun 11, 2024
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  4. Updated tags

    @nikhil
    nikhil committed Jun 11, 2024
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  5. Updated snap files with proper versions

    @nikhil
    nikhil committed Jun 11, 2024
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Commits on Jun 12, 2024

  1. readding subworkflow structure for terra development

    @rnaidu
    rnaidu committed Jun 12, 2024
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  2. Fix mutation ID

    @johnoooh
    johnoooh committed Jun 12, 2024
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  3. pushing updated work

    @rnaidu
    rnaidu committed Jun 12, 2024
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  4. subworkflow with vcf2maf module added

    @rnaidu
    rnaidu committed Jun 12, 2024
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  5. fixing vcf2maf test run

    @rnaidu
    rnaidu committed Jun 12, 2024
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  6. fixing linting checks

    @rnaidu
    rnaidu committed Jun 12, 2024
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  7. trying to fix vcf2maf test

    @rnaidu
    rnaidu committed Jun 12, 2024
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  8. adding in annotation pipeline module

    @rnaidu
    rnaidu committed Jun 12, 2024
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  9. resolving potential merge conflicts

    @rnaidu
    rnaidu committed Jun 12, 2024
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Commits on Jun 13, 2024

  1. Fixed bugs 

    Fixed bugs encountered by Nikhil.  Now should work totally for SNVs no problems.  Fixed issues in recusrsion and added a start case for recursion.
    @johnoooh
    johnoooh committed Jun 13, 2024
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  2. Merge branch 'develop' into feature/genome_nexus_final

    @rnaidu
    rnaidu authored Jun 13, 2024
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  3. Snap files for netmhc

    @johnoooh
    johnoooh committed Jun 13, 2024
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  4. Add modules_msk tag to tests

    @nikhil
    nikhil committed Jun 13, 2024
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  5. Formatting fixes for python script

    @nikhil
    nikhil committed Jun 13, 2024
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  6. More formatting fixes

    @nikhil
    nikhil committed Jun 13, 2024
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  7. Set custom phylowgs python scripts to resource scripts

    @nikhil
    nikhil committed Jun 13, 2024
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  8. Update main.nf.test.snap

    @johnoooh
    johnoooh committed Jun 13, 2024
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  9. Merge pull request #96 from mskcc-omics-workflows/feature/id_addition 

    Feature/id addition
    @nikhil
    nikhil authored Jun 13, 2024
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  10. Merge pull request #95 from mskcc-omics-workflows/feature/support_fac… 

    …ets_hisens_cncf

Update phylowgs to a new version that can parse facets hisens.cncf
    @johnoooh
    johnoooh authored Jun 13, 2024
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Commits on Jun 17, 2024

  1. fixing prettier check for meta schema json file

    @rnaidu
    rnaidu committed Jun 17, 2024
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  2. fixing prettier check for meta schema json file

    @rnaidu
    rnaidu committed Jun 17, 2024
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  3. fixing prettier check for meta schema

    @rnaidu
    rnaidu committed Jun 17, 2024
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  4. fixing prettier check for yaml schema

    @rnaidu
    rnaidu committed Jun 17, 2024
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  5. fixed prettier check for test.yml

    @rnaidu
    rnaidu committed Jun 17, 2024
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  6. fixing nf core linting checks

    @rnaidu
    rnaidu committed Jun 17, 2024
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  7. prettier check on meta yml

    @rnaidu
    rnaidu committed Jun 17, 2024
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  8. fixing nf core lint check again

    @rnaidu
    rnaidu committed Jun 17, 2024
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  9. fix lint check

    @rnaidu
    rnaidu committed Jun 17, 2024
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  10. fixing lint check again

    @rnaidu
    rnaidu committed Jun 17, 2024
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  11. Update generate_input.py

    @nikhil
    nikhil authored Jun 17, 2024
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  12. Updated snap file

    @nikhil
    nikhil committed Jun 17, 2024
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  13. Merge pull request #97 from mskcc-omics-workflows/hotfix/fix_generate… 

    …_input_id

Fix generate_input id bug
    @johnoooh
    johnoooh authored Jun 17, 2024
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  14. Some cleanup

    @nikhil
    nikhil committed Jun 17, 2024
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  15. Merge pull request #98 from mskcc-omics-workflows/feature/some_cleanup 

    Just some cleanup of print statements
    @nikhil
    nikhil authored Jun 17, 2024
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  16. Update main.nf

    buehlere committed Jun 17, 2024
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Commits on Jun 18, 2024

  1. passed vcf2maf module test

    @rnaidu
    rnaidu committed Jun 18, 2024
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  2. image cleanup

    buehlere committed Jun 18, 2024
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  3. annotation pipeline module test passed

    @rnaidu
    rnaidu committed Jun 18, 2024
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  4. passing tests on terra

    @rnaidu
    rnaidu committed Jun 18, 2024
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  5. Update main.nf.test.snap

    buehlere committed Jun 18, 2024
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  6. Update main.nf.test.snap

    buehlere committed Jun 18, 2024
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  7. Add arg for writeresults

    @nikhil
    nikhil authored Jun 18, 2024
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  8. Merge pull request #99 from mskcc-omics-workflows/feature/add_writere… 

    …sults_arg

Add arg for writeresults
    @johnoooh
    johnoooh authored Jun 18, 2024
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  9. handle NA values for cellularity

    @nikhil
    nikhil authored Jun 18, 2024
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  10. Merge pull request #100 from mskcc-omics-workflows/More-robust-cellul… 

    …arity-handling

handle NA values for cellularity
    @johnoooh
    johnoooh authored Jun 18, 2024
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  11. Update meta.yml

    @buehlere
    buehlere authored Jun 18, 2024
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  12. Update meta.yml

    @buehlere
    buehlere authored Jun 18, 2024
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Commits on Jun 19, 2024

  1. passing test snap for the subworkflow

    @rnaidu
    rnaidu committed Jun 19, 2024
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  2. getting test to pass

    @rnaidu
    rnaidu committed Jun 19, 2024
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  3. removed internal tag from annotation pipeline docker image

    @rnaidu
    rnaidu committed Jun 19, 2024
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  4. Merge branch 'feature/genome_nexus_final' of https://github.com/mskcc… 

    …-omics-workflows/modules into feature/genome_nexus_final

pulling up to date commits
    @rnaidu
    rnaidu committed Jun 19, 2024
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  5. removing trailing whitespace

    @rnaidu
    rnaidu committed Jun 19, 2024
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  6. fixed trailing whitespace and removed conda test

    @rnaidu
    rnaidu committed Jun 19, 2024
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  7. resolving annotatationpipeline test by using msk test data repo

    @rnaidu
    rnaidu committed Jun 19, 2024
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  8. updating snapshot

    @rnaidu
    rnaidu committed Jun 19, 2024
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  9. updating snapshots

    @rnaidu
    rnaidu committed Jun 19, 2024
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  10. updating all snapshots

    @rnaidu
    rnaidu committed Jun 19, 2024
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  11. update snapshot

    @rnaidu
    rnaidu committed Jun 19, 2024
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  12. snapshot update

    @rnaidu
    rnaidu committed Jun 19, 2024
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  13. Update version of neoantigenediting tools 

    - Also add scripts to module resources
    @nikhil
    nikhil committed Jun 19, 2024
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  14. Update snap files

    @nikhil
    nikhil committed Jun 19, 2024
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  15. Update neoantigenediting workflow snap

    @nikhil
    nikhil committed Jun 19, 2024
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  16. Add missing tag

    @nikhil
    nikhil committed Jun 19, 2024
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  17. Merge pull request #101 from mskcc-omics-workflows/feature/add_neoant… 

    …igen_editing_resources

Update version of neoantigenediting tools
    @johnoooh
    johnoooh authored Jun 19, 2024
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Commits on Jun 20, 2024

  1. added aligning

    @johnoooh
    johnoooh committed Jun 20, 2024
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Commits on Jun 21, 2024

  1. updated snapshots

    @rnaidu
    rnaidu committed Jun 21, 2024
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  2. fixing merge conflicts

    @rnaidu
    rnaidu committed Jun 21, 2024
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  3. fixing snapshot version

    @rnaidu
    rnaidu committed Jun 21, 2024
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Commits on Jun 24, 2024

  1. updating all snapshots

    @rnaidu
    rnaidu committed Jun 24, 2024
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  2. deleting snapshot for annotationpipeline

    @rnaidu
    rnaidu committed Jun 24, 2024
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  3. updated versions.yml tags on snapshots

    @rnaidu
    rnaidu committed Jun 24, 2024
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  4. deleting snapshot to test again

    @rnaidu
    rnaidu committed Jun 24, 2024
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  5. snapshot update

    @rnaidu
    rnaidu committed Jun 24, 2024
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  6. updated snapshot

    @rnaidu
    rnaidu committed Jun 24, 2024
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  7. added TNP fixes as well as aligning for indels

    John Orgera committed Jun 24, 2024
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  8. added print statements

    John Orgera committed Jun 24, 2024
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Commits on Jul 1, 2024

  1. Add rediscoverte test data

    @nikhil
    nikhil committed Jul 1, 2024
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  2. Add rediscoverte modules

    @nikhil
    nikhil committed Jul 1, 2024
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  3. Fixed linting

    @nikhil
    nikhil committed Jul 1, 2024
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  4. Update snap file

    @nikhil
    nikhil committed Jul 1, 2024
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  5. Add tests to ignore for conda

    @nikhil
    nikhil committed Jul 1, 2024
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  6. Fix eclint

    @nikhil
    nikhil committed Jul 1, 2024
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  7. Fix nf-core lint

    @nikhil
    nikhil committed Jul 1, 2024
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  8. Updated test files

    @nikhil
    nikhil committed Jul 1, 2024
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  9. Cleaning up

    John Orgera committed Jul 1, 2024
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  10. docker version update and snapshot update

    John Orgera committed Jul 1, 2024
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Commits on Jul 2, 2024

  1. spaces fixed

    John Orgera committed Jul 2, 2024
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  2. pace

    John Orgera committed Jul 2, 2024
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  3. Eclint fixes

    @nikhil
    nikhil committed Jul 2, 2024
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  4. Add missing tag

    @nikhil
    nikhil committed Jul 2, 2024
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  5. Merge pull request #104 from mskcc-omics-workflows/feature/indel_assi… 

    …gning

Feature/indel assigning
    @nikhil
    nikhil authored Jul 2, 2024
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  6. Set phylowgs chains to thread count

    @nikhil
    nikhil committed Jul 2, 2024
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  7. Add tool name

    @nikhil
    nikhil committed Jul 2, 2024
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  8. Some cleanup

    @nikhil
    nikhil committed Jul 2, 2024
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  9. Add optional args

    @nikhil
    nikhil committed Jul 2, 2024
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  10. Eclint fixes

    @nikhil
    nikhil committed Jul 2, 2024
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  11. Add missing tag

    @nikhil
    nikhil committed Jul 2, 2024
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  12. Merge pull request #105 from mskcc-omics-workflows/feature/set_phylow… 

    …gs_thread_chains

Set phylowgs chains to thread count
    @johnoooh
    johnoooh authored Jul 2, 2024
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  13. Merge pull request #103 from mskcc-omics-workflows/feature/add_redisc… 

    …overte

Feature/add rediscoverte
    @nikhil
    nikhil authored Jul 2, 2024
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  14. Update tags

    @nikhil
    nikhil committed Jul 2, 2024
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  15. Merge branch 'develop' into feature/update_tags

    @nikhil
    nikhil authored Jul 2, 2024
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  16. Merge pull request #106 from mskcc-omics-workflows/feature/update_tags 

    Update tags
    @nikhil
    nikhil authored Jul 2, 2024
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Commits on Jul 3, 2024

  1. Renamed data folder as data is in other gitignores

    @nikhil
    nikhil committed Jul 3, 2024
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  2. Merge pull request #107 from mskcc-omics-workflows/feature/work_with_… 

    …neoantigen_gitignore

Renamed data folder as data is in other gitignores
    @nikhil
    nikhil authored Jul 3, 2024
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Commits on Jul 8, 2024

  1. Merge branch 'develop' into Subworkflow-traceback

    @buehlere
    buehlere authored Jul 8, 2024
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  2. Fix cellularity logic for facets input

    @nikhil
    nikhil authored Jul 8, 2024
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  3. Add parsecnvs snap file

    @nikhil
    nikhil committed Jul 8, 2024
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  4. Merge pull request #108 from mskcc-omics-workflows/feature/fix_phylowgs 

    Fix cellularity logic for facets input
    @johnoooh
    johnoooh authored Jul 8, 2024
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  5. Merge branch 'develop' of github.com:mskcc-omics-workflows/modules in… 

    …to feature/add_neoantigen_modules
    @nikhil
    nikhil committed Jul 8, 2024
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  6. Add missing tag

    @nikhil
    nikhil committed Jul 8, 2024
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Commits on Jul 9, 2024

  1. tagging needs to be traceback specific 

    adjusting tagging to add traceback specific feature
    buehlere committed Jul 9, 2024
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  2. Update test.yml 

    fix test.yml
    buehlere committed Jul 9, 2024
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  3. Update test.yml

    buehlere committed Jul 9, 2024
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  4. fixing tagging name

    buehlere committed Jul 9, 2024
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  5. making samplesheet optional

    buehlere committed Jul 9, 2024
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  6. Update meta.yml

    buehlere committed Jul 9, 2024
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  7. samplesheet can't be optional

    buehlere committed Jul 9, 2024
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  8. Update main.nf

    buehlere committed Jul 9, 2024
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  9. Update main.nf

    buehlere committed Jul 9, 2024
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Commits on Jul 10, 2024

  1. Update main.nf

    buehlere committed Jul 10, 2024
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  2. docs cleanup

    buehlere committed Jul 10, 2024
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  3. Update meta.yml

    buehlere committed Jul 10, 2024
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  4. PR cleanup

    buehlere committed Jul 10, 2024
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Commits on Jul 11, 2024

  1. Merge branch 'develop' into feature/add-readme

    @buehlere
    buehlere authored Jul 11, 2024
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  2. updated docker image of annotationpipeline to latest release and rera… 

    …n tests
    @rnaidu
    rnaidu committed Jul 11, 2024
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  3. Merge branch 'develop' into feature/genome_nexus_final

    @rnaidu
    rnaidu authored Jul 11, 2024
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  4. Merge pull request #58 from mskcc-omics-workflows/feature/genome_nexu… 

    …s_final

Subworkflow: genome nexus - vcf2maf + annotationpipeline
    @rnaidu
    rnaidu authored Jul 11, 2024
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Commits on Jul 12, 2024

  1. Merge branch 'develop' into feature/add-readme

    @rhshah
    rhshah authored Jul 12, 2024
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  2. Merge pull request #94 from mskcc-omics-workflows/feature/add-readme 

    Adding README
    @rhshah
    rhshah authored Jul 12, 2024
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  3. addressed Eric's issues

    John Orgera committed Jul 12, 2024
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Commits on Jul 13, 2024

  1. Merge branch 'develop' into feature/add_neoantigen_modules

    @buehlere
    buehlere authored Jul 13, 2024
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  2. Merge branch 'develop' into Subworkflow-traceback

    @buehlere
    buehlere authored Jul 13, 2024
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  3. Update yaml-schema.json

    buehlere committed Jul 13, 2024
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Commits on Jul 14, 2024

  1. Add resource folder to prettier ignore

    @nikhil
    nikhil committed Jul 14, 2024
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  2. Fix dangling space

    @nikhil
    nikhil committed Jul 14, 2024
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  3. Merge branch 'feature/add_neoantigen_modules' of github.com:mskcc-omi… 

    …cs-workflows/modules into feature/add_neoantigen_modules
    @nikhil
    nikhil committed Jul 14, 2024
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Commits on Jul 15, 2024

  1. fix netmhcstabpan

    @johnoooh
    johnoooh authored Jul 15, 2024
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  2. Update netmhcpan

    @johnoooh
    johnoooh authored Jul 15, 2024
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  3. update versions

    @johnoooh
    johnoooh authored Jul 15, 2024
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Commits on Jul 18, 2024

  1. Update meta.yml 

    Small change to restart tests
    @johnoooh
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  2. Merge pull request #110 from mskcc-omics-workflows/feature/add_neoant… 

    …igen_modules

Feature/add neoantigen modules
    @johnoooh
    johnoooh authored Jul 18, 2024
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Commits on Jul 22, 2024

  1. Fix tag sample count

    @nikhil
    nikhil committed Jul 22, 2024
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  2. Set index to use high resources

    @nikhil
    nikhil committed Jul 22, 2024
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Commits on Jul 23, 2024

  1. Merge pull request #115 from mskcc-omics-workflows/feature/small_fixe… 

    …s_for_rediscoverte

Small fixes for rediscoverte
    @nikhil
    nikhil authored Jul 23, 2024
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Commits on Jul 24, 2024

  1. adding main, still need tests

    John Orgera committed Jul 24, 2024
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  2. Convert added

    @johnoooh
    johnoooh committed Jul 24, 2024
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  3. test passing

    @johnoooh
    johnoooh committed Jul 24, 2024
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  4. Merge branch 'develop' into Subworkflow-traceback

    @buehlere
    buehlere authored Jul 24, 2024
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  5. linting

    @johnoooh
    johnoooh committed Jul 24, 2024
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  6. more linting

    @johnoooh
    johnoooh committed Jul 24, 2024
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  7. Update environment.yml

    @johnoooh
    johnoooh committed Jul 24, 2024
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  8. Updating version file

    @johnoooh
    johnoooh committed Jul 24, 2024
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  9. new version out

    @johnoooh
    johnoooh committed Jul 24, 2024
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  10. test fix ?

    @johnoooh
    johnoooh committed Jul 24, 2024
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  11. Merge pull request #47 from mskcc-omics-workflows/Subworkflow-traceback 

    Subworkflow:traceback
    @buehlere
    buehlere authored Jul 24, 2024
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Commits on Jul 25, 2024

  1. changed versioning of annotation pipeline module in genome nexus subw… 

    …orkflow to latest release
    @rnaidu
    rnaidu committed Jul 25, 2024
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  2. Merge branch 'develop' into feature/neoTSV

    @nikhil
    nikhil authored Jul 25, 2024
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  3. working tests for annotationpipeline after updating versioning

    @rnaidu
    rnaidu committed Jul 25, 2024
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  4. Merge branch 'develop' into hotfix/update-test-datasets

    @buehlere
    buehlere authored Jul 25, 2024
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  5. Merge pull request #118 from mskcc-omics-workflows/genomenexus_versio… 

    …ning

changed versioning of annotation pipeline module in genome nexus subw…
    @rnaidu
    rnaidu authored Jul 25, 2024
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  6. Update java vm args

    @nikhil
    nikhil authored Jul 25, 2024
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  7. Merge pull request #121 from mskcc-omics-workflows/feature/update_jav… 

    …a_vm_args

Update java vm args
    @rnaidu
    rnaidu authored Jul 25, 2024
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  8. Merge branch 'develop' into feature/ppflagfixer

    @huyu335
    huyu335 authored Jul 25, 2024
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  9. Merge pull request #43 from mskcc-omics-workflows/feature/ppflagfixer 

    Module:ppflagfixer
    @huyu335
    huyu335 authored Jul 25, 2024
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  10. Merge branch 'develop' into hotfix/update-test-datasets

    @huyu335
    huyu335 authored Jul 25, 2024
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Commits on Jul 30, 2024

  1. Fix stub test for formatnetmhcpan

    @nikhil
    nikhil committed Jul 30, 2024
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  2. Merge branch 'develop' into feature/fix_formatnetmhcpan_stub_test

    @nikhil
    nikhil authored Jul 30, 2024
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  3. Merge pull request #123 from mskcc-omics-workflows/feature/fix_format… 

    …netmhcpan_stub_test

Fix stub test for formatnetmhcpan
    @johnoooh
    johnoooh authored Jul 30, 2024
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Commits on Aug 1, 2024

  1. Merge branch 'develop' into feature/neoTSV

    @johnoooh
    johnoooh authored Aug 1, 2024
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  2. Merge pull request #117 from mskcc-omics-workflows/feature/neoTSV 

    Feature/neo tsv
    @johnoooh
    johnoooh authored Aug 1, 2024
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Commits on Aug 12, 2024

  1. Merge branch 'develop' into hotfix/update-test-datasets

    @huyu335
    huyu335 authored Aug 12, 2024
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  2. Merge pull request #92 from mskcc-omics-workflows/hotfix/update-test-… 

    …datasets

Hotfix/update test dataset links
    @huyu335
    huyu335 authored Aug 12, 2024
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Commits on Aug 26, 2024

  1. Merge branch 'main' into release/0.1.1

    @buehlere
    buehlere authored Aug 26, 2024
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  2. Update test bam locations

    @huyu335
    huyu335 authored Aug 26, 2024
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  3. Merge pull request #131 from mskcc-omics-workflows/hotfix/ppflagfixer 

    Update test bam locations
    @huyu335
    huyu335 authored Aug 26, 2024
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Commits on Aug 27, 2024

  1. Merge branch 'develop' into release/0.1.1

    buehlere committed Aug 27, 2024
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