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

CHORES: update all modules #1304

Merged
merged 21 commits into from
Nov 3, 2023
Merged

CHORES: update all modules #1304

merged 21 commits into from
Nov 3, 2023

Commits on Nov 1, 2023

  1. update all modules (will probably break things)

    @maxulysse
    maxulysse committed Nov 1, 2023
    Configuration menu
    Copy the full SHA
    9d15b23 View commit details
    Browse the repository at this point in the history

  2. simpler patch for bcftools-annotate

    @maxulysse
    maxulysse committed Nov 1, 2023
    Configuration menu
    Copy the full SHA
    bc1b3bd View commit details
    Browse the repository at this point in the history

  3. finish proper patching of bcftools/annotate

    @maxulysse
    maxulysse committed Nov 1, 2023
    Configuration menu
    Copy the full SHA
    795c2a5 View commit details
    Browse the repository at this point in the history

  4. restore patch for controlfreec/assesssignificance

    @maxulysse
    maxulysse committed Nov 1, 2023
    Configuration menu
    Copy the full SHA
    49b55bd View commit details
    Browse the repository at this point in the history

  5. restore patch for dragmap/hashtable

    @maxulysse
    maxulysse committed Nov 1, 2023
    Configuration menu
    Copy the full SHA
    b7b0720 View commit details
    Browse the repository at this point in the history

  6. update CHANGELOG

    @maxulysse
    maxulysse committed Nov 1, 2023
    Configuration menu
    Copy the full SHA
    7bae363 View commit details
    Browse the repository at this point in the history

  7. update CHANGELOG

    @maxulysse
    maxulysse committed Nov 1, 2023
    Configuration menu
    Copy the full SHA
    994a84a View commit details
    Browse the repository at this point in the history

  8. fix bcfann tests

    @maxulysse
    maxulysse committed Nov 1, 2023
    Configuration menu
    Copy the full SHA
    1021445 View commit details
    Browse the repository at this point in the history

  9. fix channels for bcftools/mpileup

    @maxulysse
    maxulysse committed Nov 1, 2023
    Configuration menu
    Copy the full SHA
    c00d630 View commit details
    Browse the repository at this point in the history

  10. fix channels for cnvkit/batch

    @maxulysse
    maxulysse committed Nov 1, 2023
    Configuration menu
    Copy the full SHA
    78f311a View commit details
    Browse the repository at this point in the history

  11. fix channels for manta

    @maxulysse
    maxulysse committed Nov 1, 2023
    Configuration menu
    Copy the full SHA
    2f0747a View commit details
    Browse the repository at this point in the history

  12. if the vcf.gz changes on rerun, pretty sure the vcf.gz.tbi does the same

    @maxulysse
    maxulysse committed Nov 1, 2023
    Configuration menu
    Copy the full SHA
    cccc364 View commit details
    Browse the repository at this point in the history

  13. no need for --download_cache here

    @maxulysse
    maxulysse committed Nov 1, 2023
    Configuration menu
    Copy the full SHA
    6cf72f4 View commit details
    Browse the repository at this point in the history

Commits on Nov 2, 2023

  1. update gatk4spark modules and subworkflows

    @maxulysse
    maxulysse committed Nov 2, 2023
    Configuration menu
    Copy the full SHA
    a60b744 View commit details
    Browse the repository at this point in the history

  2. Update subworkflows/local/bam_applybqsr_spark/main.nf

    @maxulysse
    maxulysse authored Nov 2, 2023
    Configuration menu
    Copy the full SHA
    72a45b9 View commit details
    Browse the repository at this point in the history

  3. update base.config

    @maxulysse
    maxulysse committed Nov 2, 2023
    Configuration menu
    Copy the full SHA
    1501fa4 View commit details
    Browse the repository at this point in the history

  4. add info about changed names

    @maxulysse
    maxulysse committed Nov 2, 2023
    Configuration menu
    Copy the full SHA
    f8ecd4e View commit details
    Browse the repository at this point in the history

  5. rename tag to gatk4spark

    @maxulysse
    maxulysse committed Nov 2, 2023
    Configuration menu
    Copy the full SHA
    745e415 View commit details
    Browse the repository at this point in the history

Commits on Nov 3, 2023

  1. fix config

    @maxulysse
    maxulysse committed Nov 3, 2023
    Configuration menu
    Copy the full SHA
    202ebd9 View commit details
    Browse the repository at this point in the history

  2. '' ->

    @maxulysse
    maxulysse committed Nov 3, 2023
    Configuration menu
    Copy the full SHA
    63348f7 View commit details
    Browse the repository at this point in the history

  3. exclude failing nf-tests due to missing data from modules

    @maxulysse
    maxulysse committed Nov 3, 2023
    Configuration menu
    Copy the full SHA
    8b1b2e9 View commit details
    Browse the repository at this point in the history