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

Condense, improve and clean up Nextflow logging #25

Merged
merged 11 commits into from
Aug 23, 2021
Merged

Condense, improve and clean up Nextflow logging #25

merged 11 commits into from
Aug 23, 2021

Commits on Aug 23, 2021

  1. Condense, improve and clean up Nextflow logging 

    - tries to remedy visual issues in ANSI console by condensing and
  shortening line lengths of log output
- improves some wording, consistency and whitespacing of log output
- refactor some log output code into functions
- adds ksrates version to log
    @lohausr
    lohausr committed Aug 23, 2021
    Configuration menu
    Copy the full SHA
    45b0cd3 View commit details
    Browse the repository at this point in the history

  2. Don't clean up if ksrates config file newly generated 

    There won't be anything to clean up, and onComplete would print
irrelevant warning about empty focal_species parameter.
    @lohausr
    lohausr committed Aug 23, 2021
    Configuration menu
    Copy the full SHA
    2bf281b View commit details
    Browse the repository at this point in the history

  3. Single '/' in logs folder path when focal_species empty

    @lohausr
    lohausr committed Aug 23, 2021
    Configuration menu
    Copy the full SHA
    5261d4a View commit details
    Browse the repository at this point in the history

  4. Small fix: remove debug log.info

    @lohausr
    lohausr committed Aug 23, 2021
    Configuration menu
    Copy the full SHA
    3590b94 View commit details
    Browse the repository at this point in the history

  5. Some minor rewording and code cleanup

    @lohausr
    lohausr committed Aug 23, 2021
    Configuration menu
    Copy the full SHA
    39017d2 View commit details
    Browse the repository at this point in the history

  6. Add missing process name changes

    @lohausr
    lohausr committed Aug 23, 2021
    Configuration menu
    Copy the full SHA
    c252234 View commit details
    Browse the repository at this point in the history

  7. Some renaming of channels and variables 

    - Correction -> Adjustment
- peakCalling -> paralogsAnalyses
    @lohausr
    lohausr committed Aug 23, 2021
    Configuration menu
    Copy the full SHA
    4f5e8db View commit details
    Browse the repository at this point in the history

  8. Bugfix clean up when new ksrates config file

    @lohausr
    lohausr committed Aug 23, 2021
    Configuration menu
    Copy the full SHA
    8b2dda6 View commit details
    Browse the repository at this point in the history

  9. Update error_box2

    @Cecilia-Sensalari
    Cecilia-Sensalari committed Aug 23, 2021
    Configuration menu
    Copy the full SHA
    23fcac9 View commit details
    Browse the repository at this point in the history

  10. Merge branch 'master' into nextflow_log

    @Cecilia-Sensalari
    Cecilia-Sensalari committed Aug 23, 2021
    Configuration menu
    Copy the full SHA
    71a0d5e View commit details
    Browse the repository at this point in the history

  11. Merge branch 'nextflow_log' of https://github.com/VIB-PSB/ksrates int… 

    …o nextflow_log
    @Cecilia-Sensalari
    Cecilia-Sensalari committed Aug 23, 2021
    Configuration menu
    Copy the full SHA
    cfe6bb3 View commit details
    Browse the repository at this point in the history