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

upstream: Align trim #2

Merged
merged 25 commits into from
Mar 8, 2024
Merged

upstream: Align trim #2

merged 25 commits into from
Mar 8, 2024

Commits on Jan 25, 2021

  1. adding --min-depth flag to minion and parameterising the mask and sta… 

    …ts calls with it
    @will-rowe
    will-rowe committed Jan 25, 2021
    Configuration menu
    Copy the full SHA
    895e744 View commit details
    Browse the repository at this point in the history

  2. parameterising the vcf filter with the same global min-depth variable… 

    … for consistency
    @will-rowe
    will-rowe committed Jan 25, 2021
    Configuration menu
    Copy the full SHA
    ecaa8fa View commit details
    Browse the repository at this point in the history

  3. adding github actions CI

    @will-rowe
    will-rowe committed Jan 25, 2021
    Configuration menu
    Copy the full SHA
    b2a0019 View commit details
    Browse the repository at this point in the history

  4. adding github actions CI

    @will-rowe
    will-rowe committed Jan 25, 2021
    Configuration menu
    Copy the full SHA
    23537f5 View commit details
    Browse the repository at this point in the history

  5. adding github actions CI

    @will-rowe
    will-rowe committed Jan 25, 2021
    Configuration menu
    Copy the full SHA
    61bc87a View commit details
    Browse the repository at this point in the history

  6. adding github actions CI

    @will-rowe
    will-rowe committed Jan 25, 2021
    Configuration menu
    Copy the full SHA
    30a408b View commit details
    Browse the repository at this point in the history

  7. moving unit tests over to github actions

    @will-rowe
    will-rowe committed Jan 25, 2021
    Configuration menu
    Copy the full SHA
    695a880 View commit details
    Browse the repository at this point in the history

  8. parameterising the vcf filter with the same global min-depth variable… 

    … for consistency
    @will-rowe
    will-rowe committed Jan 25, 2021
    Configuration menu
    Copy the full SHA
    9a40aa0 View commit details
    Browse the repository at this point in the history

  9. replacing travis with github action CI

    @will-rowe
    will-rowe committed Jan 25, 2021
    Configuration menu
    Copy the full SHA
    9d6388b View commit details
    Browse the repository at this point in the history

  10. adding DOI to README

    @will-rowe
    will-rowe committed Jan 25, 2021
    Configuration menu
    Copy the full SHA
    0dbe838 View commit details
    Browse the repository at this point in the history

  11. updating artic-tools, adding more stats to artic report, running repo… 

    …rt regardless of strict, setting strict to filter VCF
    @will-rowe
    will-rowe committed Jan 25, 2021
    Configuration menu
    Copy the full SHA
    d849b61 View commit details
    Browse the repository at this point in the history

  12. adding opt to enforce full length amplicon match during align trim, a… 

    …ctivate using --strict flag to minion
    @will-rowe
    will-rowe committed Jan 25, 2021
    Configuration menu
    Copy the full SHA
    b6c26a9 View commit details
    Browse the repository at this point in the history

  13. tweaking report generator

    @will-rowe
    will-rowe committed Jan 25, 2021
    Configuration menu
    Copy the full SHA
    b0526ea View commit details
    Browse the repository at this point in the history

  14. version bump

    @will-rowe
    will-rowe committed Jan 25, 2021
    Configuration menu
    Copy the full SHA
    8d15e3c View commit details
    Browse the repository at this point in the history

Commits on Jan 27, 2021

  1. docs update

    @will-rowe
    will-rowe committed Jan 27, 2021
    Configuration menu
    Copy the full SHA
    584dd37 View commit details
    Browse the repository at this point in the history

Commits on Feb 2, 2021

  1. replacing longshot with the latest medaka

    @will-rowe
    will-rowe committed Feb 2, 2021
    Configuration menu
    Copy the full SHA
    2ffd9ae View commit details
    Browse the repository at this point in the history

  2. trying to fix medaka install on osx

    @will-rowe
    will-rowe committed Feb 2, 2021
    Configuration menu
    Copy the full SHA
    21510e5 View commit details
    Browse the repository at this point in the history

  3. adding bcftools norm command to remove vars from the pass VCF if they… 

    … have been masked out in the preconsensus
    @will-rowe
    will-rowe committed Feb 2, 2021
    Configuration menu
    Copy the full SHA
    7398995 View commit details
    Browse the repository at this point in the history

  4. cleaner parsing of GQ field

    @will-rowe
    will-rowe committed Feb 2, 2021
    Configuration menu
    Copy the full SHA
    1226043 View commit details
    Browse the repository at this point in the history

Commits on Feb 8, 2021

  1. upgrading to latest medaka and dropping longshot from the conda env

    @will-rowe
    will-rowe committed Feb 8, 2021
    Configuration menu
    Copy the full SHA
    bd4f327 View commit details
    Browse the repository at this point in the history

Commits on Feb 10, 2021

  1. exposing opts for vcf_filter

    @will-rowe
    will-rowe committed Feb 10, 2021
    Configuration menu
    Copy the full SHA
    fd6d066 View commit details
    Browse the repository at this point in the history

Commits on Feb 17, 2021

  1. bumping medaka to latest patch

    @will-rowe
    will-rowe committed Feb 17, 2021
    Configuration menu
    Copy the full SHA
    3b90202 View commit details
    Browse the repository at this point in the history

Commits on Feb 18, 2021

  1. unpinning pandas

    @will-rowe
    will-rowe committed Feb 18, 2021
    Configuration menu
    Copy the full SHA
    d86d913 View commit details
    Browse the repository at this point in the history

Commits on Feb 22, 2021

  1. Change to overlap-based method of amplicon resolution

    @cjw85
    cjw85 committed Feb 22, 2021
    Configuration menu
    Copy the full SHA
    dfe4e9a View commit details
    Browse the repository at this point in the history

Commits on Feb 23, 2021

  1. Integrate new align_trim.py

    @cjw85
    cjw85 committed Feb 23, 2021
    Configuration menu
    Copy the full SHA
    d0b2182 View commit details
    Browse the repository at this point in the history