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

fix: rename-contigs to include target bed intersection and add mapping files to resources #73

Merged
merged 21 commits into from
Apr 22, 2024
Merged

fix: rename-contigs to include target bed intersection and add mapping files to resources #73

merged 21 commits into from
Apr 22, 2024

Commits on Apr 16, 2024

  1. feat: add rename-contigs resources

    @famosab
    famosab committed Apr 16, 2024
    Configuration menu
    Copy the full SHA
    c8aab2b View commit details
    Browse the repository at this point in the history

  2. fix: make normalize_calls standalone and add bedtools intersect

    @famosab
    famosab committed Apr 16, 2024
    Configuration menu
    Copy the full SHA
    5039a8f View commit details
    Browse the repository at this point in the history

  3. fix: output in vcf.gz

    @famosab
    famosab committed Apr 16, 2024
    Configuration menu
    Copy the full SHA
    53401a4 View commit details
    Browse the repository at this point in the history

  4. test: norm params

    @famosab
    famosab committed Apr 16, 2024
    Configuration menu
    Copy the full SHA
    a6c6c60 View commit details
    Browse the repository at this point in the history

  5. Merge branch 'main' into fix/rename-contigs

    @johanneskoester
    johanneskoester authored Apr 16, 2024
    Configuration menu
    Copy the full SHA
    58c6903 View commit details
    Browse the repository at this point in the history

  6. fix: correct commands

    @famosab
    famosab committed Apr 16, 2024
    Configuration menu
    Copy the full SHA
    58c8b2e View commit details
    Browse the repository at this point in the history

  7. Merge branch 'fix/rename-contigs' of https://github.com/snakemake-wor… 

    …kflows/dna-seq-benchmark into fix/rename-contigs
    @famosab
    famosab committed Apr 16, 2024
    Configuration menu
    Copy the full SHA
    c2bf53d View commit details
    Browse the repository at this point in the history

  8. test: switch from confidence to target regions

    @famosab
    famosab committed Apr 16, 2024
    Configuration menu
    Copy the full SHA
    1415c89 View commit details
    Browse the repository at this point in the history

  9. fix: linting

    @famosab
    famosab committed Apr 16, 2024
    Configuration menu
    Copy the full SHA
    1824a5b View commit details
    Browse the repository at this point in the history

Commits on Apr 17, 2024

  1. fix: start with intersect and pipe into norm

    @famosab
    famosab committed Apr 17, 2024
    Configuration menu
    Copy the full SHA
    8eec88b View commit details
    Browse the repository at this point in the history

  2. test: giab dummy

    @famosab
    famosab committed Apr 17, 2024
    Configuration menu
    Copy the full SHA
    b68c6ba View commit details
    Browse the repository at this point in the history

  3. test: target instead of confidence regions

    @famosab
    famosab committed Apr 17, 2024
    Configuration menu
    Copy the full SHA
    e66c82e View commit details
    Browse the repository at this point in the history

  4. fix: remove output from view

    @famosab
    famosab committed Apr 17, 2024
    Configuration menu
    Copy the full SHA
    d495233 View commit details
    Browse the repository at this point in the history

  5. fix: add giab dummy again

    @famosab
    famosab committed Apr 17, 2024
    Configuration menu
    Copy the full SHA
    9320bde View commit details
    Browse the repository at this point in the history

  6. fix: added get_norm_params because of extra param for limit reads in … 

    …test cases
    @BiancaStoecker
    BiancaStoecker committed Apr 17, 2024
    Configuration menu
    Copy the full SHA
    50a3fe4 View commit details
    Browse the repository at this point in the history

  7. Merge branch 'main' into fix/rename-contigs

    @BiancaStoecker
    BiancaStoecker authored Apr 17, 2024
    Configuration menu
    Copy the full SHA
    a66de79 View commit details
    Browse the repository at this point in the history

Commits on Apr 18, 2024

  1. fix: remove unused checks for confidence regions

    @famosab
    famosab committed Apr 18, 2024
    Configuration menu
    Copy the full SHA
    9800da9 View commit details
    Browse the repository at this point in the history

Commits on Apr 22, 2024

  1. fix: f String use

    @famosab
    famosab committed Apr 22, 2024
    Configuration menu
    Copy the full SHA
    866e281 View commit details
    Browse the repository at this point in the history

  2. fix: f string use for benchmark_name

    @famosab
    famosab authored Apr 22, 2024
    Configuration menu
    Copy the full SHA
    0ce5adb View commit details
    Browse the repository at this point in the history

  3. fix: fix benchmark name

    @BiancaStoecker
    BiancaStoecker committed Apr 22, 2024
    Configuration menu
    Copy the full SHA
    78508ed View commit details
    Browse the repository at this point in the history

  4. fix: fix previous commit

    @BiancaStoecker
    BiancaStoecker committed Apr 22, 2024
    Configuration menu
    Copy the full SHA
    4379e55 View commit details
    Browse the repository at this point in the history