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Update SV branch from main #21

Merged
merged 46 commits into from
Feb 14, 2024
Merged

Update SV branch from main #21

merged 46 commits into from
Feb 14, 2024

Commits on Jan 24, 2024

  1. Update README.md 

    Rename cohort, start adding description
    @oneillkza
    oneillkza authored Jan 24, 2024
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Commits on Feb 12, 2024

  1. Add files via upload

    @epleasance
    epleasance authored Feb 12, 2024
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  2. Update rmd.Dockerfile 

    Added ggplot and alluvial packages
    @epleasance
    epleasance authored Feb 12, 2024
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  3. Apply automatic changes

    @epleasance @github-actions
    epleasance authored and github-actions[bot] committed Feb 12, 2024
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  4. Merge pull request #8 from bcgsc/cohort 

    Cohort
    @oneillkza
    oneillkza authored Feb 12, 2024
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  5. Update renderRMarkdown.yaml 

    Adjust to re-run checks on edited PRs.
    @oneillkza
    oneillkza authored Feb 12, 2024
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  6. Update renderJupyter.yaml

    @oneillkza
    oneillkza authored Feb 12, 2024
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  7. Apply automatic changes

    @oneillkza @github-actions
    oneillkza authored and github-actions[bot] committed Feb 12, 2024
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  8. Merge pull request #9 from bcgsc/oneillkza-patch-2 

    Oneillkza patch 2
    @oneillkza
    oneillkza authored Feb 12, 2024
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  9. Update README.md 

    Set badge to be linked to the main branch only, not the latest check on any branch.
    @oneillkza
    oneillkza authored Feb 12, 2024
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  10. Update renderRMarkdown.yaml 

    Add on workflow_dispatch to trigger on main branch.
    @oneillkza
    oneillkza authored Feb 12, 2024
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Commits on Feb 13, 2024

  1. Update README.md 

    Add Docker container badges; add detailed text.
    @oneillkza
    oneillkza authored Feb 13, 2024
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  2. Merge pull request #11 from bcgsc/main 

    Update patch branch from main
    @oneillkza
    oneillkza authored Feb 13, 2024
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  3. Apply automatic changes

    @oneillkza @github-actions
    oneillkza authored and github-actions[bot] committed Feb 13, 2024
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  4. Merge pull request #10 from bcgsc/oneillkza-patch-1 

    Updates to readme and rendering
    @oneillkza
    oneillkza authored Feb 13, 2024
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  5. add ecDNA files in correct directory

    @oneillkza
    oneillkza committed Feb 13, 2024
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  6. add ecDNA dependencies

    @oneillkza
    oneillkza committed Feb 13, 2024
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  7. fix missing dependency

    @oneillkza
    oneillkza committed Feb 13, 2024
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  8. remove View commands that can run when compiling Rmd

    @oneillkza
    oneillkza committed Feb 13, 2024
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  9. missing dependency ggsurvfit

    @oneillkza
    oneillkza committed Feb 13, 2024
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  10. bump actions versions for new Node

    @oneillkza
    oneillkza committed Feb 13, 2024
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  11. disambiguate select; change in container seems to have broken this?

    @oneillkza
    oneillkza committed Feb 13, 2024
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  12. another Node-related version bump

    @oneillkza
    oneillkza committed Feb 13, 2024
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Commits on Feb 14, 2024

  1. Try using fread instead of read_delim to see if it solves timeout iss… 

    …ues.
    @oneillkza
    oneillkza committed Feb 14, 2024
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  2. Add dependency needed to read gz files

    @oneillkza
    oneillkza committed Feb 14, 2024
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  3. typo

    @oneillkza
    oneillkza committed Feb 14, 2024
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  4. Try converting to data.table to see if it solves weird GitHub-only ob… 

    …ject 'anonymous_sample_ID_tumour' not found error
    @oneillkza
    oneillkza committed Feb 14, 2024
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  5. Switch to github_document as output format so as to keep md files

    @oneillkza
    oneillkza committed Feb 14, 2024
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  6. Try some other things to solve this GitHub Actions-only error.

    @oneillkza
    oneillkza committed Feb 14, 2024
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  7. Apply automatic changes

    @oneillkza @github-actions
    oneillkza authored and github-actions[bot] committed Feb 14, 2024
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  8. Merge pull request #17 from bcgsc/ecDNA_fixed 

    Ecdna fixed up pull request; also fixed some issues wtih ASE timing out (use of data.table seems to help) and a weird dplyr issue in the cohort figure.
    @oneillkza
    oneillkza authored Feb 14, 2024
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  9. Add Fig. 5I files

    @sigmaclennan
    sigmaclennan authored Feb 14, 2024
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  10. Apply automatic changes

    @oneillkza @github-actions
    oneillkza authored and github-actions[bot] committed Feb 14, 2024
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  11. Apply automatic changes

    @sigmaclennan @github-actions
    sigmaclennan authored and github-actions[bot] committed Feb 14, 2024
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  12. Upload phasing Rmd

    @epleasance
    epleasance authored Feb 14, 2024
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  13. Update rmd.Dockerfile

    @epleasance
    epleasance authored Feb 14, 2024
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  14. resolve conflict

    @oneillkza
    oneillkza committed Feb 14, 2024
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  15. Apply automatic changes

    @oneillkza @github-actions
    oneillkza authored and github-actions[bot] committed Feb 14, 2024
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  16. Update Phasing_figures.Rmd - display plots

    @epleasance
    epleasance authored Feb 14, 2024
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  17. Update Phasing_figures.Rmd

    @epleasance
    epleasance authored Feb 14, 2024
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  18. Apply automatic changes

    @epleasance @github-actions
    epleasance authored and github-actions[bot] committed Feb 14, 2024
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  19. Merge pull request #20 from bcgsc/phasing 

    Phasing figure code
    @oneillkza
    oneillkza authored Feb 14, 2024
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  20. try to fix conflict over generated files

    @oneillkza
    oneillkza committed Feb 14, 2024
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  21. try to fix conflict over generated files

    @oneillkza
    oneillkza committed Feb 14, 2024
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  22. Merge pull request #19 from bcgsc/main 

    Update from main branch
    @oneillkza
    oneillkza authored Feb 14, 2024
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  23. Merge pull request #18 from bcgsc/ecDNA_5I 

    Add Fig. 5I files
    @oneillkza
    oneillkza authored Feb 14, 2024
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