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

Expand GTF filtering to remove rows with empty transcript ID when required, fix STAR GTF usage #1107

Merged
merged 48 commits into from
Nov 15, 2023
Merged

Expand GTF filtering to remove rows with empty transcript ID when required, fix STAR GTF usage #1107

merged 48 commits into from
Nov 15, 2023

Commits on Nov 7, 2023

  1. Add special GTF handling for stringtie

    @pinin4fjords
    pinin4fjords committed Nov 7, 2023
    Configuration menu
    Copy the full SHA
    688d19b View commit details
    Browse the repository at this point in the history

  2. Update CHANGELOG

    @pinin4fjords
    pinin4fjords committed Nov 7, 2023
    Configuration menu
    Copy the full SHA
    c6d354d View commit details
    Browse the repository at this point in the history

  3. appease eclint

    @pinin4fjords
    pinin4fjords committed Nov 7, 2023
    Configuration menu
    Copy the full SHA
    82b67e1 View commit details
    Browse the repository at this point in the history

  4. Comment dollar

    @pinin4fjords
    pinin4fjords committed Nov 7, 2023
    Configuration menu
    Copy the full SHA
    5dbbe0c View commit details
    Browse the repository at this point in the history

Commits on Nov 8, 2023

  1. Fix multiqc to avoid imp module error

    @pinin4fjords
    pinin4fjords committed Nov 8, 2023
    Configuration menu
    Copy the full SHA
    124c570 View commit details
    Browse the repository at this point in the history

Commits on Nov 9, 2023

  1. Actually, unify GTF filtering

    @pinin4fjords
    pinin4fjords committed Nov 9, 2023
    Configuration menu
    Copy the full SHA
    57d4bde View commit details
    Browse the repository at this point in the history

  2. Reverse test profile change

    @pinin4fjords
    pinin4fjords committed Nov 9, 2023
    Configuration menu
    Copy the full SHA
    7908ca3 View commit details
    Browse the repository at this point in the history

  3. misc fixes

    @pinin4fjords
    pinin4fjords committed Nov 9, 2023
    Configuration menu
    Copy the full SHA
    f791e8a View commit details
    Browse the repository at this point in the history

  4. Blackify

    @pinin4fjords
    pinin4fjords committed Nov 9, 2023
    Configuration menu
    Copy the full SHA
    19a72f6 View commit details
    Browse the repository at this point in the history

  5. move module to right path

    @pinin4fjords
    pinin4fjords committed Nov 9, 2023
    Configuration menu
    Copy the full SHA
    2cfea9d View commit details
    Browse the repository at this point in the history

  6. update changelog

    @pinin4fjords
    pinin4fjords committed Nov 9, 2023
    Configuration menu
    Copy the full SHA
    9b4e140 View commit details
    Browse the repository at this point in the history

  7. Correct selector

    @pinin4fjords
    pinin4fjords committed Nov 9, 2023
    Configuration menu
    Copy the full SHA
    ec6f80e View commit details
    Browse the repository at this point in the history

  8. Make gtf filtering dependent on gtf

    @pinin4fjords
    pinin4fjords committed Nov 9, 2023
    Configuration menu
    Copy the full SHA
    25324ba View commit details
    Browse the repository at this point in the history

  9. Fix multiqc to avoid imp module error

    @pinin4fjords
    pinin4fjords committed Nov 9, 2023
    Configuration menu
    Copy the full SHA
    26e9c1c View commit details
    Browse the repository at this point in the history

  10. Fix transcript_id pattern

    @pinin4fjords
    pinin4fjords committed Nov 9, 2023
    Configuration menu
    Copy the full SHA
    251e368 View commit details
    Browse the repository at this point in the history

  11. blackify

    @pinin4fjords
    pinin4fjords committed Nov 9, 2023
    Configuration menu
    Copy the full SHA
    6a3ea7e View commit details
    Browse the repository at this point in the history

  12. emit chromosome-filtered gtf from genome preparation

    @pinin4fjords
    pinin4fjords committed Nov 9, 2023
    Configuration menu
    Copy the full SHA
    bb47808 View commit details
    Browse the repository at this point in the history

  13. [skip ci] fix changelog

    @pinin4fjords
    pinin4fjords committed Nov 9, 2023
    Configuration menu
    Copy the full SHA
    047f749 View commit details
    Browse the repository at this point in the history

  14. Merge branch 'stringtie_gtf' of github.com:nf-core/rnaseq into string… 

    …tie_gtf
    @pinin4fjords
    pinin4fjords committed Nov 9, 2023
    Configuration menu
    Copy the full SHA
    4153d4a View commit details
    Browse the repository at this point in the history

  15. Thank myself to poke CI

    @pinin4fjords
    pinin4fjords committed Nov 9, 2023
    Configuration menu
    Copy the full SHA
    a801013 View commit details
    Browse the repository at this point in the history

Commits on Nov 10, 2023

  1. Merge branch 'stringtie_gtf' of github.com:nf-core/rnaseq into string… 

    …tie_gtf
    @pinin4fjords
    pinin4fjords committed Nov 10, 2023
    Configuration menu
    Copy the full SHA
    910ad75 View commit details
    Browse the repository at this point in the history

  2. filter_gtf improvements

    @pinin4fjords
    pinin4fjords committed Nov 10, 2023
    Configuration menu
    Copy the full SHA
    16430c2 View commit details
    Browse the repository at this point in the history

  3. Blackify

    @pinin4fjords
    pinin4fjords committed Nov 10, 2023
    Configuration menu
    Copy the full SHA
    65ac5ef View commit details
    Browse the repository at this point in the history

  4. [skip ci] Add resolved issues to changelog

    @pinin4fjords
    pinin4fjords committed Nov 10, 2023
    Configuration menu
    Copy the full SHA
    c4823ea View commit details
    Browse the repository at this point in the history

  5. Merge branch 'dev' into stringtie_gtf

    @pinin4fjords
    pinin4fjords committed Nov 10, 2023
    Configuration menu
    Copy the full SHA
    c2842dc View commit details
    Browse the repository at this point in the history

  6. Merge remote-tracking branch 'origin/dev' into stringtie_gtf

    @pinin4fjords
    pinin4fjords committed Nov 10, 2023
    Configuration menu
    Copy the full SHA
    7a977bb View commit details
    Browse the repository at this point in the history

  7. reinstate publish modes

    @pinin4fjords
    pinin4fjords committed Nov 10, 2023
    Configuration menu
    Copy the full SHA
    ecb3a14 View commit details
    Browse the repository at this point in the history

Commits on Nov 14, 2023

  1. [skip ci] Reduce logging in GTF filtering

    @pinin4fjords
    pinin4fjords committed Nov 14, 2023
    Configuration menu
    Copy the full SHA
    1c23a4a View commit details
    Browse the repository at this point in the history

  2. [skip ci] Apply suggestions from code review 

    Co-authored-by: Matthias Zepper <6963520+MatthiasZepper@users.noreply.github.com>
    @pinin4fjords @MatthiasZepper
    pinin4fjords and MatthiasZepper authored Nov 14, 2023
    Configuration menu
    Copy the full SHA
    0a70d58 View commit details
    Browse the repository at this point in the history

  3. [skip ci] post-suggestion integration work

    @pinin4fjords
    pinin4fjords committed Nov 14, 2023
    Configuration menu
    Copy the full SHA
    996abcc View commit details
    Browse the repository at this point in the history

  4. [skip ci] more post-review tidy-up to GTF filtering script

    @pinin4fjords
    pinin4fjords committed Nov 14, 2023
    Configuration menu
    Copy the full SHA
    01e05f7 View commit details
    Browse the repository at this point in the history

  5. [skip ci] reinstate logging

    @pinin4fjords
    pinin4fjords committed Nov 14, 2023
    Configuration menu
    Copy the full SHA
    556af91 View commit details
    Browse the repository at this point in the history

  6. [skip ci] reinstate logging

    @pinin4fjords
    pinin4fjords committed Nov 14, 2023
    Configuration menu
    Copy the full SHA
    ad998c4 View commit details
    Browse the repository at this point in the history

  7. [skip ci] Fix salmon subworkflow call for gtf

    @pinin4fjords
    pinin4fjords committed Nov 14, 2023
    Configuration menu
    Copy the full SHA
    80a9543 View commit details
    Browse the repository at this point in the history

  8. [skip ci] also raise value for no transcript ids

    @pinin4fjords
    pinin4fjords committed Nov 14, 2023
    Configuration menu
    Copy the full SHA
    519e42a View commit details
    Browse the repository at this point in the history

  9. [skip ci] @drpatelh feedback: Try to avoid filtering process where no… 

    …t required
    @pinin4fjords
    pinin4fjords committed Nov 14, 2023
    Configuration menu
    Copy the full SHA
    5e1378e View commit details
    Browse the repository at this point in the history

Commits on Nov 15, 2023

  1. Simplify GTF filtering

    @pinin4fjords
    pinin4fjords committed Nov 15, 2023
    Configuration menu
    Copy the full SHA
    fb70fdf View commit details
    Browse the repository at this point in the history

  2. Blackify

    @pinin4fjords
    pinin4fjords committed Nov 15, 2023
    Configuration menu
    Copy the full SHA
    5c213c5 View commit details
    Browse the repository at this point in the history

  3. Document GTF filtering

    @pinin4fjords
    pinin4fjords committed Nov 15, 2023
    Configuration menu
    Copy the full SHA
    6d55142 View commit details
    Browse the repository at this point in the history

  4. [automated] Fix linting with Prettier

    @nf-core-bot
    nf-core-bot committed Nov 15, 2023
    Configuration menu
    Copy the full SHA
    6e1454b View commit details
    Browse the repository at this point in the history

  5. Merge branch 'dev' into stringtie_gtf

    @pinin4fjords
    pinin4fjords authored Nov 15, 2023
    Configuration menu
    Copy the full SHA
    d1ce4f9 View commit details
    Browse the repository at this point in the history

  6. Bump modules config for merged module

    @pinin4fjords
    pinin4fjords committed Nov 15, 2023
    Configuration menu
    Copy the full SHA
    aff1d2e View commit details
    Browse the repository at this point in the history

  7. Bump pipeline version to 3.13.0

    @drpatelh
    drpatelh committed Nov 15, 2023
    Configuration menu
    Copy the full SHA
    f7d078c View commit details
    Browse the repository at this point in the history

  8. [skip ci] Changes from local review

    @drpatelh
    drpatelh committed Nov 15, 2023
    Configuration menu
    Copy the full SHA
    1c6012e View commit details
    Browse the repository at this point in the history

  9. Move --skip_* parameters to the same section

    @drpatelh
    drpatelh committed Nov 15, 2023
    Configuration menu
    Copy the full SHA
    e7126c8 View commit details
    Browse the repository at this point in the history

  10. [skip ci] Tidy up code block

    @drpatelh
    drpatelh committed Nov 15, 2023
    Configuration menu
    Copy the full SHA
    13cc0e9 View commit details
    Browse the repository at this point in the history

  11. Move filter_gtf logic into main workflow

    @drpatelh
    drpatelh committed Nov 15, 2023
    Configuration menu
    Copy the full SHA
    3ac4a3a View commit details
    Browse the repository at this point in the history

  12. [automated] Fix linting with Prettier

    @nf-core-bot
    nf-core-bot committed Nov 15, 2023
    Configuration menu
    Copy the full SHA
    b67558d View commit details
    Browse the repository at this point in the history