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

CNVKit 0.9.10 update #3651

Merged
merged 10 commits into from
Jul 21, 2023
Merged

CNVKit 0.9.10 update #3651

merged 10 commits into from
Jul 21, 2023

Commits on Jun 22, 2023

  1. upgrade CNVkit to 0.9.10

    @priesgo
    priesgo committed Jun 22, 2023
    Configuration menu
    Copy the full SHA
    b7e667d View commit details
    Browse the repository at this point in the history

  2. homogenise keywords of all CNVkit modules

    @priesgo
    priesgo committed Jun 22, 2023
    Configuration menu
    Copy the full SHA
    b220ab7 View commit details
    Browse the repository at this point in the history

Commits on Jul 12, 2023

  1. Add samtools dependency to bam2seqz module of sequenzautils 

    Without specifying the dependency to a more or less current version of samtools, conda solves the environment for sequenza by using a very old samtools version that can cause problems when processing subsampled files (automated tests)
    @JulianMohr
    JulianMohr committed Jul 12, 2023
    Configuration menu
    Copy the full SHA
    b7c2f13 View commit details
    Browse the repository at this point in the history

Commits on Jul 19, 2023

  1. Update cnvkit to 0.9.10 

    Changes:
 - Update cnvkit to 0.9.10
 - Update samtools in cnvkit modules to 1.17

Based on #3545 authored by @priesgo.
    @adamrtalbot
    adamrtalbot committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    29cf715 View commit details
    Browse the repository at this point in the history

  2. Merge branch 'master' into cnvkit_0.9.10_updates

    @adamrtalbot
    adamrtalbot committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    e5262ab View commit details
    Browse the repository at this point in the history

  3. cnvkit 0.9.10 test update

    @adamrtalbot
    adamrtalbot committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    1bff597 View commit details
    Browse the repository at this point in the history

Commits on Jul 21, 2023

  1. update checksums of output files in tests for CNVkit batch

    @priesgo
    priesgo committed Jul 21, 2023
    Configuration menu
    Copy the full SHA
    88aa48c View commit details
    Browse the repository at this point in the history

  2. Merge branch 'master' into cnvkit_0.9.10_updates

    @priesgo
    priesgo committed Jul 21, 2023
    Configuration menu
    Copy the full SHA
    66709d9 View commit details
    Browse the repository at this point in the history

  3. Update cnvkit/export VCF test

    @adamrtalbot
    adamrtalbot committed Jul 21, 2023
    Configuration menu
    Copy the full SHA
    a77412d View commit details
    Browse the repository at this point in the history

  4. Additional tags for sequenzautils

    @adamrtalbot
    adamrtalbot committed Jul 21, 2023
    Configuration menu
    Copy the full SHA
    57d30ea View commit details
    Browse the repository at this point in the history