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 streptococcus workflow #352

Draft
wants to merge 25 commits into
base: master
Choose a base branch
from
Draft

Add streptococcus workflow #352

wants to merge 25 commits into from

Commits on Sep 18, 2024

  1. Add emmtyper to Makefile

    @ryanjameskennedy
    ryanjameskennedy committed Sep 18, 2024
    Configuration menu
    Copy the full SHA
    ceadaf6 View commit details
    Browse the repository at this point in the history

Commits on Sep 19, 2024

  1. Add streptococcus profiles

    @ryanjameskennedy
    ryanjameskennedy committed Sep 19, 2024
    Configuration menu
    Copy the full SHA
    160964e View commit details
    Browse the repository at this point in the history

  2. Add emmtyper module

    @ryanjameskennedy
    ryanjameskennedy committed Sep 19, 2024
    Configuration menu
    Copy the full SHA
    40a1454 View commit details
    Browse the repository at this point in the history

Commits on Sep 21, 2024

  1. Update Makefile re streptococcus

    @ryanjameskennedy
    ryanjameskennedy committed Sep 21, 2024
    Configuration menu
    Copy the full SHA
    30ec693 View commit details
    Browse the repository at this point in the history

Commits on Sep 22, 2024

  1. Fixes for streptococcus Makefile installation

    @ryanjameskennedy
    ryanjameskennedy committed Sep 22, 2024
    Configuration menu
    Copy the full SHA
    3273324 View commit details
    Browse the repository at this point in the history

Commits on Sep 23, 2024

  1. Add spyogenes

    @ryanjameskennedy
    ryanjameskennedy committed Sep 23, 2024
    Configuration menu
    Copy the full SHA
    3e37efd View commit details
    Browse the repository at this point in the history

Commits on Sep 24, 2024

  1. Update amrfinder taxon cmd

    @ryanjameskennedy
    ryanjameskennedy committed Sep 24, 2024
    Configuration menu
    Copy the full SHA
    3fb437c View commit details
    Browse the repository at this point in the history

  2. Fix when commands

    @ryanjameskennedy
    ryanjameskennedy committed Sep 24, 2024
    Configuration menu
    Copy the full SHA
    0b56a52 View commit details
    Browse the repository at this point in the history

  3. Fix --species cmd

    @ryanjameskennedy
    ryanjameskennedy committed Sep 24, 2024
    Configuration menu
    Copy the full SHA
    d2c8351 View commit details
    Browse the repository at this point in the history

  4. Update base and main workflows re strep

    @ryanjameskennedy
    ryanjameskennedy committed Sep 24, 2024
    Configuration menu
    Copy the full SHA
    f3aab8c View commit details
    Browse the repository at this point in the history

  5. Add get_taxon methods

    @ryanjameskennedy
    ryanjameskennedy committed Sep 24, 2024
    Configuration menu
    Copy the full SHA
    d435231 View commit details
    Browse the repository at this point in the history

  6. Add streptococcus workflow

    @ryanjameskennedy
    ryanjameskennedy committed Sep 24, 2024
    Configuration menu
    Copy the full SHA
    854b9c1 View commit details
    Browse the repository at this point in the history

  7. Update streptococcus config

    @ryanjameskennedy
    ryanjameskennedy committed Sep 24, 2024
    Configuration menu
    Copy the full SHA
    265673e View commit details
    Browse the repository at this point in the history

  8. Reset make install rules after testing

    @ryanjameskennedy
    ryanjameskennedy committed Sep 24, 2024
    Configuration menu
    Copy the full SHA
    bd9fff5 View commit details
    Browse the repository at this point in the history

Commits on Sep 25, 2024

  1. Add emmtyper to strep pipelines

    @ryanjameskennedy
    ryanjameskennedy committed Sep 25, 2024
    Configuration menu
    Copy the full SHA
    c6f6dca View commit details
    Browse the repository at this point in the history

  2. Move serotypefinder & shigapass to typing

    @ryanjameskennedy
    ryanjameskennedy committed Sep 25, 2024
    Configuration menu
    Copy the full SHA
    3dee1df View commit details
    Browse the repository at this point in the history

Commits on Sep 26, 2024

  1. Module bug fixes

    @ryanjameskennedy
    ryanjameskennedy committed Sep 26, 2024
    Configuration menu
    Copy the full SHA
    f29bc7f View commit details
    Browse the repository at this point in the history

Commits on Sep 30, 2024

  1. Add emmtyper to configs

    @ryanjameskennedy
    ryanjameskennedy committed Sep 30, 2024
    Configuration menu
    Copy the full SHA
    194ddff View commit details
    Browse the repository at this point in the history

  2. Remove when commands

    @ryanjameskennedy
    ryanjameskennedy committed Sep 30, 2024
    Configuration menu
    Copy the full SHA
    d4c3263 View commit details
    Browse the repository at this point in the history

  3. Fix Chewbacca inputs

    @ryanjameskennedy
    ryanjameskennedy committed Sep 30, 2024
    Configuration menu
    Copy the full SHA
    e80220a View commit details
    Browse the repository at this point in the history

  4. Change spyogenes genome from GCF_900475035.1 to GCF_000006785.2

    @ryanjameskennedy
    ryanjameskennedy committed Sep 30, 2024
    Configuration menu
    Copy the full SHA
    74bcc4c View commit details
    Browse the repository at this point in the history

Commits on Oct 1, 2024

  1. Fix resfinder species arg

    @ryanjameskennedy
    ryanjameskennedy committed Oct 1, 2024
    Configuration menu
    Copy the full SHA
    a4baca6 View commit details
    Browse the repository at this point in the history

  2. Resolve empty channel bug

    @ryanjameskennedy
    ryanjameskennedy committed Oct 1, 2024
    Configuration menu
    Copy the full SHA
    d121885 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'master' of github.com:genomic-medicine-sweden/jasen int… 

    …o 304-add-streptococcus-workflow
    @ryanjameskennedy
    ryanjameskennedy committed Oct 1, 2024
    Configuration menu
    Copy the full SHA
    56d33e2 View commit details
    Browse the repository at this point in the history

  4. Update CHANGELOG re streptococcus

    @ryanjameskennedy
    ryanjameskennedy committed Oct 1, 2024
    Configuration menu
    Copy the full SHA
    4bf4f5e View commit details
    Browse the repository at this point in the history