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Release/0.1.2#156

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buehlere merged 187 commits intomainmskcc-omics-workflows/modules:mainfrom release/0.1.2mskcc-omics-workflows/modules:release/0.1.2Copy head branch name to clipboardNov 27, 2024

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Commits on Aug 1, 2024

• testdata edited

  

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• dding all the neosv files

  

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• passing tests

  

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• snap file added

  

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• tag changed

  

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• meta changes

  

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• prettier ran

  

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• whitespace

  

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• conda exclude

  

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• Merge branch 'develop' into feature/neosv

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Commits on Aug 21, 2024

• all changes, still working on tests

  

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• netmhcpan test

  

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• Merge branch 'feature/neosv' of https://github.com/mskcc-omics-workflows/modules into feature/neosv

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• Update main.nf

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Commits on Aug 26, 2024

• tests fixing

  

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• Merge branch 'feature/neosv' of https://github.com/mskcc-omics-workflows/modules into feature/neosv

  

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• Merge branch 'develop' into feature/neosv

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Commits on Aug 27, 2024

• changed tests

  

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• Merge branch 'feature/neosv' of https://github.com/mskcc-omics-workflows/modules into feature/neosv

  

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Commits on Aug 28, 2024

• meta changes

  

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• prettier done

  

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• whitespace`

  

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• whitespace issues

  

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• Merge branch 'develop' into feature/neosv

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• test fix

  

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• Merge branch 'feature/neosv' of https://github.com/mskcc-omics-workflows/modules into feature/neosv

  

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• Merge branch 'develop' into feature/neosv

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• Update generate_input.py

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• Add git pull before commit

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• fix format issue

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• change depth

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• update message

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• remove test

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• add duplicate checks

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• debug location of subworkflow

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Commits on Aug 29, 2024

• Merge pull request #136 from mskcc-omics-workflows/hotfix/git-commit-race-condition

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• Merge branch 'develop' into feature/neosv

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• Merge pull request #124 from mskcc-omics-workflows/feature/neosv

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Commits on Sep 6, 2024

• test push

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• updating subworkflow and modules for genome nexus with working version in nucleovar

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• updated tests for genome nexus subworkflow and modules

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• updated subworkflow and modules for genome nexus

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• Merge branch 'develop' into genome_nexus_lint_update

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• test update

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• removed redundancy from environment.yml files

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• committing environment.yml files as is to demonstrate name field error

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• removing name field as mandatory from environment-schema.json to pass updated nf-core lint functionality

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Commits on Sep 9, 2024

• final environment_schema.json file for changes made in new nf-core linting update. Users will have to edit current module environment.yml files accordingly. future modules downloaded by nf-core wil…

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• Merge pull request #143 from mskcc-omics-workflows/feature/remove_name_from_schema

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• updated environment.yml files for genome nexus modules since environment_schema.json was updated in develop branch in order to pass nf-core lint checks

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• Merge branch 'develop' into genome_nexus_lint_update

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• added versioning in versions.yml output

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• Merge branch 'genome_nexus_lint_update' of https://github.com/mskcc-omics-workflows/modules into genome_nexus_lint_update

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• added versioning to versions.yml output

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• updated snapshot for genomenexus/annotationpipeline

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• removed text file

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• Merge pull request #141 from mskcc-omics-workflows/genome_nexus_lint_update

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Commits on Sep 10, 2024

• made updates to mutect1 module to match local changes made for nucleovar

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• first commit to start PR

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• removal of test text file

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• Merge pull request #144 from mskcc-omics-workflows/mutect1_lint_update

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  rnaidu

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• updating traceback subworkflow with local changes made to pass nf-core lint

  rnaidu

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• updated traceback subworkflow and genotypevariants module to reflect local changes made in order to pass nf-core lint check

  rnaidu

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• updated snapshot for traceback subworkflow

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• updating snapshots again

  rnaidu

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• update snapshot

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• snapshot for subworkflow

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• snapshots

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• removing snapshots to see if test passes

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• added in snapshots

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• reran snapshots

  rnaidu

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• added StageAs in pvmaf concat module to avoid input file name collision

  rnaidu

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• modified second assertion in traceback subworkflow test, updated snapshot, and updated pvmaf concat environment.yml

  rnaidu

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• removed extraneous test.tap file

  rnaidu

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• updated snapshots

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Commits on Sep 11, 2024

• Merge pull request #145 from mskcc-omics-workflows/traceback_lint_update

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Commits on Sep 30, 2024

• Allow num_chains to be set in the config

  nikhil

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• Removed yaml schema tag

  nikhil

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• Fix yml schemas

  nikhil

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• Set schema to modules directory

  nikhil

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• Update to work with the new schema

  nikhil

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• Update scheme some more

  nikhil

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• Update output name

  nikhil

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Commits on Oct 1, 2024

• updated traceback subworkflow and associated modules with changes for nucleovar version 1

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• updated meta and environment.ymls for traceback associated modulees to pass updated nf-core linting schema checks.

  rnaidu

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• passing prettier and editorconfig checks

  rnaidu

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• updated snapshot for pvmaf/concat module

  rnaidu

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• updating meta.yml so it is in sync with local copy in nucleovar

  rnaidu

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Commits on Oct 4, 2024

• Adding AGPL license

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• Update test.yml

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• Update test.yml

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• Update test.yml

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• Update test.yml

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• Update test.yml

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• Update yaml to md

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• Missed one place

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• update json schemas

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• reformat

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Commits on Oct 30, 2024

• Merge pull request #151 from mskcc-omics-workflows/feature/update-md-workflow

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• Merge branch 'develop' into feature/add-license

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• Merge pull request #150 from mskcc-omics-workflows/feature/add-license

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• Merge branch 'develop' into feature/phylowgs_config_num_chains

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Commits on Nov 1, 2024

• big lint fix

  

  buehlere

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Commits on Nov 13, 2024

• Merge branch 'develop' into traceback2_lint_update

  

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• Merge pull request #149 from mskcc-omics-workflows/traceback2_lint_update

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Commits on Nov 14, 2024

• Merge branch 'develop' into feature/phylowgs_config_num_chains

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• Merge pull request #148 from mskcc-omics-workflows/feature/phylowgs_config_num_chains

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• Renamed module to netmhcpan4 and updated docs

  nikhil

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• Update formatnetmhcpan to handle netmhcpan3

  nikhil

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• Cleanup input generation script

  nikhil

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• Cleanup generateMutFasta script

  nikhil

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• Add netmhcpan3

  nikhil

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• cleanup generate_input script

  nikhil

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• Fix bug in input id generation

  nikhil

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• Merge branch 'develop' of github.com:mskcc-omics-workflows/modules into neoantigen

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Commits on Nov 19, 2024

• Rename netmhcpan3 module

  nikhil

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• Linting fixes for various modules

  nikhil

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• Merge branch 'develop' of github.com:mskcc-omics-workflows/modules into fix_lint

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• removed extra "channels:"

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• removed extra channels: again

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• removed extra channels: again x2

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• removed extra channels: x3

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• Update environment.yml

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• removed extra channels: x4

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• Merge branch 'fix_lint' of github.com:mskcc-omics-workflows/modules into neoantigen

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• Merge pull request #157 from mskcc-omics-workflows/fix_lint

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• Merge pull request #163 from mskcc-omics-workflows/develop

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• Adding codeowners action

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• Update generate_codeowners.sh

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• Update assign_codeowners.yml

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• Fixes for commits and shell script

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• Update generate_codeowners.sh

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• Update CODEOWNERS file

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• Update generate_codeowners.sh

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• Merge branch 'feature/add_codeowners' of https://github.com/mskcc-omics-workflows/modules into feature/add_codeowners

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• Update generate_codeowners.sh

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• Update CODEOWNERS file

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• Update generate_codeowners.sh

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• Merge branch 'feature/add_codeowners' of https://github.com/mskcc-omics-workflows/modules into feature/add_codeowners

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• Update CODEOWNERS file

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• Update assign_codeowners.yml

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• Merge branch 'feature/add_codeowners' of https://github.com/mskcc-omics-workflows/modules into feature/add_codeowners

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Commits on Nov 21, 2024

• Update conda skip list

  nikhil

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• Updated test data

  nikhil

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• Neoantigen util script updates

  nikhil

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• Add netmhc3 module

  nikhil

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• Set netmhcpan to netmhcpan4

  nikhil

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• Update output metadata for netmhcstabpan

  nikhil

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• Update paths in subworkflow

  nikhil

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• Merge branch 'develop' into neoantigen

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• Merge pull request #164 from mskcc-omics-workflows/feature/add_codeowners

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Commits on Nov 25, 2024

• Add option to select netmhc version in subworkflow

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• Update neoantigenutils output metadata

  nikhil

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• Update module and tests for netmhc3

  nikhil

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• Update module and tests for netmhcpan4

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• Update module and tests for netmhcstabpan

  nikhil

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• Made module meta prettier

  nikhil

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• Fix linting errors

  nikhil

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• Merge branch 'develop' into neoantigen

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• Update CODEOWNERS file

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• Meta.yml fixes

  nikhil

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• Merge branch 'neoantigen' of github.com:mskcc-omics-workflows/modules into neoantigen

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• More fixes for meta.yml

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