Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Control-FREEC improvements #204

Merged
merged 34 commits into from
May 18, 2020
Merged

Control-FREEC improvements #204

merged 34 commits into from
May 18, 2020

Commits on May 15, 2020

  1. added script to help downstream analysis, adding RankScore for Scout

    @maxulysse
    Szilveszter Juhos authored and maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    cb13187 View commit details
    Browse the repository at this point in the history

  2. nf-core bump-version . 2.5.1 

    fix script name in docs

fix markdownlint

fix autoMounts in singularity profile, closes nf-core#48

build 2.5.1 version of annotation containers

update CHANGELOG

Typo

Update .github/workflows/branch.yml

Update .github/workflows/branch.yml

Update README.md
    @maxulysse
    maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    8551b2f View commit details
    Browse the repository at this point in the history

  3. reducing CPU usage for Mpileup 

    cleanup with meld

some docs additions

Update docs/downstream.md

Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>

Update docs/downstream.md

Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>

added extra space

Update docs/downstream.md

Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>

Update docs/downstream.md

Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>

Update docs/downstream.md

Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>

Update docs/downstream.md

Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>

Update docs/downstream.md

Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>

Update docs/downstream.md

Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
    @maxulysse
    Szilveszter Juhos and maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    fc1dd2f View commit details
    Browse the repository at this point in the history

  4. First time CF is working with extra pileups

    @maxulysse
    Szilveszter Juhos authored and maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    3b11389 View commit details
    Browse the repository at this point in the history

  5. yet an other version that somehow worked

    @maxulysse
    Szilveszter Juhos authored and maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    203b756 View commit details
    Browse the repository at this point in the history

  6. remove --normal_pileup and --tumor_pileup params

    @maxulysse
    maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    fd80e8c View commit details
    Browse the repository at this point in the history

  7. update freebayes germline command

    @ggabernet @maxulysse
    ggabernet authored and maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    fad7a6a View commit details
    Browse the repository at this point in the history

  8. update changelog

    @ggabernet @maxulysse
    ggabernet authored and maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    3929a67 View commit details
    Browse the repository at this point in the history

  9. fix --save_bam_mapped + small typos

    @maxulysse
    maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    5a62d50 View commit details
    Browse the repository at this point in the history

  10. update CHANGELOG

    @maxulysse
    maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    455fd06 View commit details
    Browse the repository at this point in the history

  11. add step controlfreec

    @maxulysse
    maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    815c36e View commit details
    Browse the repository at this point in the history

  12. use nf-core header

    @maxulysse
    maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    fa09b3d View commit details
    Browse the repository at this point in the history

  13. update config

    @maxulysse
    maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    b46f4e2 View commit details
    Browse the repository at this point in the history

  14. cleanup

    @maxulysse
    maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    5f6eabc View commit details
    Browse the repository at this point in the history

  15. add mappability files to igenomes

    @maxulysse
    maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    04cb2cd View commit details
    Browse the repository at this point in the history

  16. better name for tsv file

    @maxulysse
    maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    e5a27b4 View commit details
    Browse the repository at this point in the history

  17. fix output directory

    @maxulysse
    maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    c514c3f View commit details
    Browse the repository at this point in the history

  18. enable usage of - in names of tools or steps

    @maxulysse
    maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    50a584c View commit details
    Browse the repository at this point in the history

  19. better default for coefficientofvariation

    @maxulysse
    maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    38dd289 View commit details
    Browse the repository at this point in the history

  20. improve help

    @maxulysse
    maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    c7aec1a View commit details
    Browse the repository at this point in the history

  21. First working version 

    Removing nf-core#51 and moving downstream to szilvajuhos/btb-scripts
    @maxulysse
    Szilveszter Juhos authored and maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    5d9e995 View commit details
    Browse the repository at this point in the history

  22. Fixing some null parameters and C&P typos

    @maxulysse
    Szilveszter Juhos authored and maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    1983576 View commit details
    Browse the repository at this point in the history

  23. update and reorder params

    @maxulysse
    maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    1ca1c5a View commit details
    Browse the repository at this point in the history

  24. reorder and update params

    @maxulysse
    maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    57cfad7 View commit details
    Browse the repository at this point in the history

  25. update and reorder params

    @maxulysse
    maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    1692e5a View commit details
    Browse the repository at this point in the history

  26. update docs

    @maxulysse
    maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    cda438b View commit details
    Browse the repository at this point in the history

  27. fix prepare_recalibration step

    @maxulysse
    maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    4a1cf40 View commit details
    Browse the repository at this point in the history

  28. update CHANGELOG

    @maxulysse
    maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    5b5d1dc View commit details
    Browse the repository at this point in the history

  29. Apply suggestions from code review

    @maxulysse
    maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    4e0a5f5 View commit details
    Browse the repository at this point in the history

  30. use only one cpu to generate mpileup for controlfreec

    @maxulysse
    maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    f59bcd0 View commit details
    Browse the repository at this point in the history

  31. fix conflicts

    @maxulysse
    maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    23c2086 View commit details
    Browse the repository at this point in the history

  32. spacing

    @maxulysse
    maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    8226fd6 View commit details
    Browse the repository at this point in the history

  33. fix merge conflicts

    @maxulysse
    maxulysse committed May 15, 2020
    Configuration menu
    Copy the full SHA
    9a3ef3d View commit details
    Browse the repository at this point in the history

Commits on May 18, 2020

  1. if step = controlfreec then tools is controlfreec

    @maxulysse
    maxulysse committed May 18, 2020
    Configuration menu
    Copy the full SHA
    edd53b1 View commit details
    Browse the repository at this point in the history