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Subworkflow: genome nexus - vcf2maf + annotationpipeline #58

Merged
merged 69 commits into from
Jul 11, 2024
Merged

Subworkflow: genome nexus - vcf2maf + annotationpipeline #58

merged 69 commits into from
Jul 11, 2024

Commits on Mar 18, 2024

  1. added module and documentation for genome nexus vcf2maf

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    rnaidu committed Mar 18, 2024
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  2. disabling conda test in test.yml

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    rnaidu committed Mar 18, 2024
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  3. ran prettier on directory

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    rnaidu committed Mar 18, 2024
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  4. disabled conda nf-test

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    rnaidu committed Mar 18, 2024
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Commits on Apr 3, 2024

  1. made changes based on PR comments

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    rnaidu committed Apr 3, 2024
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  2. Merge branch 'develop' into feature/genome_nexus_final

    @rnaidu
    rnaidu authored Apr 3, 2024
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  3. resolving failing tests

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    rnaidu committed Apr 3, 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

avoiding merge conflicts
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    rnaidu committed Apr 3, 2024
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Commits on Apr 4, 2024

  1. resolving nf test errors

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    rnaidu committed Apr 4, 2024
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  2. adding empty array line to pytest_modules.yml to pass nf-core lint check

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    rnaidu committed Apr 4, 2024
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Commits on May 13, 2024

  1. replaced vcf2maf with vcf2maflite in MSK-module

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

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

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

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    rnaidu committed May 13, 2024
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  5. fixing trailspace errors

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    rnaidu committed May 13, 2024
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Commits on Jun 6, 2024

  1. merged annotation pipeline module branch into the final genome nexus … 

    …branch. subworkflow will be built off of here
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    rnaidu committed Jun 6, 2024
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  2. 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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  3. 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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  4. created genome nexus subworkflow locally and pushing to branch

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    rnaidu committed Jun 6, 2024
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  5. 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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  6. adding tested annotation pipeline module for genome nexus subworkflow

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

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

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    rnaidu committed Jun 6, 2024
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  9. fixing prettier check

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    rnaidu committed Jun 6, 2024
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Commits on Jun 12, 2024

  1. readding subworkflow structure for terra development

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    rnaidu committed Jun 12, 2024
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  2. pushing updated work

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

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

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    rnaidu committed Jun 12, 2024
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  5. fixing linting checks

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

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

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    rnaidu committed Jun 12, 2024
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  8. resolving potential merge conflicts

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

  1. Merge branch 'develop' into feature/genome_nexus_final

    @rnaidu
    rnaidu authored Jun 13, 2024
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Commits on Jun 17, 2024

  1. fixing prettier check for meta schema json file

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    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

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

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

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    rnaidu committed Jun 17, 2024
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  9. fix lint check

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

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

  1. passed vcf2maf module test

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    rnaidu committed Jun 18, 2024
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  2. annotation pipeline module test passed

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

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    rnaidu committed Jun 18, 2024
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Commits on Jun 19, 2024

  1. passing test snap for the subworkflow

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

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

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    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
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    rnaidu committed Jun 19, 2024
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  5. removing trailing whitespace

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    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

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    rnaidu committed Jun 19, 2024
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  9. updating snapshots

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    rnaidu committed Jun 19, 2024
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  10. updating all snapshots

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    rnaidu committed Jun 19, 2024
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  11. update snapshot

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    rnaidu committed Jun 19, 2024
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  12. snapshot update

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    rnaidu committed Jun 19, 2024
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Commits on Jun 21, 2024

  1. updated snapshots

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    rnaidu committed Jun 21, 2024
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  2. fixing merge conflicts

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    rnaidu committed Jun 21, 2024
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  3. fixing snapshot version

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

  1. updating all snapshots

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

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

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

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    rnaidu committed Jun 24, 2024
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  5. snapshot update

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    rnaidu committed Jun 24, 2024
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  6. updated snapshot

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    rnaidu committed Jun 24, 2024
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Commits on Jul 11, 2024

  1. updated docker image of annotationpipeline to latest release and rera… 

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

    @rnaidu
    rnaidu authored Jul 11, 2024
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