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

Add support for generating taxprofiler/funcscan input samplesheets for preprocessed FASTQs/FASTAs #688

Draft
wants to merge 19 commits into
base: dev
Choose a base branch
from
Draft

Add support for generating taxprofiler/funcscan input samplesheets for preprocessed FASTQs/FASTAs #688

wants to merge 19 commits into from

Commits on Oct 10, 2024

  1. first draft push with TODOs

    @vagkaratzas
    vagkaratzas committed Oct 10, 2024
    Configuration menu
    Copy the full SHA
    2a48e7f View commit details
    Browse the repository at this point in the history

  2. first attempt, files not yet being published in outdir

    @vagkaratzas
    vagkaratzas committed Oct 10, 2024
    Configuration menu
    Copy the full SHA
    3b80e0c View commit details
    Browse the repository at this point in the history

  3. 4 conditions for different short reads outdirs

    @vagkaratzas
    vagkaratzas committed Oct 10, 2024
    Configuration menu
    Copy the full SHA
    2bd8352 View commit details
    Browse the repository at this point in the history

  4. Add funcscan code

    @jasmezz
    jasmezz committed Oct 10, 2024
    Configuration menu
    Copy the full SHA
    a744175 View commit details
    Browse the repository at this point in the history

  5. Generate multiple samplesheets

    @jasmezz
    jasmezz committed Oct 10, 2024
    Configuration menu
    Copy the full SHA
    8672790 View commit details
    Browse the repository at this point in the history

  6. Update multi-samplesheet generation

    @jasmezz
    jasmezz committed Oct 10, 2024
    Configuration menu
    Copy the full SHA
    be91462 View commit details
    Browse the repository at this point in the history

Commits on Oct 14, 2024

  1. Update docs [skip ci] 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @jasmezz @jfy133
    jasmezz and jfy133 authored Oct 14, 2024
    Configuration menu
    Copy the full SHA
    e9df126 View commit details
    Browse the repository at this point in the history

Commits on Oct 15, 2024

  1. Added channelToSamplesheet function to subworkflow, added nf-test (no… 

    …t run yet)
    @vagkaratzas
    vagkaratzas committed Oct 15, 2024
    Configuration menu
    Copy the full SHA
    e441e76 View commit details
    Browse the repository at this point in the history

  2. Validate samplesheet generation parameters, null defaults,

    @vagkaratzas
    vagkaratzas committed Oct 15, 2024
    Configuration menu
    Copy the full SHA
    ddb9c96 View commit details
    Browse the repository at this point in the history

  3. nf-test updated (no snapshot yet)

    @vagkaratzas
    vagkaratzas committed Oct 15, 2024
    Configuration menu
    Copy the full SHA
    bf11fb3 View commit details
    Browse the repository at this point in the history

  4. Update function and minor tweaks

    @jfy133
    jfy133 committed Oct 15, 2024
    Configuration menu
    Copy the full SHA
    8724961 View commit details
    Browse the repository at this point in the history

  5. Merge branch 'dev' into samplsheet-for-taxprofiler

    @jfy133
    jfy133 authored Oct 15, 2024
    Configuration menu
    Copy the full SHA
    b354da9 View commit details
    Browse the repository at this point in the history

  6. Put the if/else within the function, not as an argument to the function

    @jfy133
    jfy133 committed Oct 15, 2024
    Configuration menu
    Copy the full SHA
    f6b9a99 View commit details
    Browse the repository at this point in the history

  7. Fix name of file,remove duplicated check

    @jfy133
    jfy133 committed Oct 15, 2024
    Configuration menu
    Copy the full SHA
    bec8347 View commit details
    Browse the repository at this point in the history

  8. Only check save_clipped_reads if taxprofiler in pipeline list

    @jfy133
    jfy133 committed Oct 15, 2024
    Configuration menu
    Copy the full SHA
    67958ec View commit details
    Browse the repository at this point in the history

Commits on Oct 16, 2024

  1. Fix logic for generating taxprofiler paths; make new channel to pass … 

    …correct assemblies files (Funcsan)
    @jfy133
    jfy133 committed Oct 16, 2024
    Configuration menu
    Copy the full SHA
    997674a View commit details
    Browse the repository at this point in the history

Commits on Oct 24, 2024

  1. Merge remote-tracking branch 'upstream/dev' into samplsheet-for-taxpr… 

    …ofiler
    @jfy133
    jfy133 committed Oct 24, 2024
    Configuration menu
    Copy the full SHA
    aa71298 View commit details
    Browse the repository at this point in the history

  2. Compelte template merge

    @jfy133
    jfy133 committed Oct 24, 2024
    Configuration menu
    Copy the full SHA
    0163690 View commit details
    Browse the repository at this point in the history

Commits on Oct 27, 2024

  1. Merge branch 'dev' into samplsheet-for-taxprofiler

    @jfy133
    jfy133 authored Oct 27, 2024
    Configuration menu
    Copy the full SHA
    535747c View commit details
    Browse the repository at this point in the history