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

Release v2.4.0 #256

Merged
merged 52 commits into from
Aug 24, 2023
Merged

Release v2.4.0 #256

merged 52 commits into from
Aug 24, 2023

Commits on Jun 7, 2023

  1. fix: file collision when using cellranger

    @adamrtalbot
    adamrtalbot committed Jun 7, 2023
    Configuration menu
    Copy the full SHA
    8ec2dd0 View commit details
    Browse the repository at this point in the history

  2. Add cellranger to continuous tests

    @adamrtalbot
    adamrtalbot committed Jun 7, 2023
    Configuration menu
    Copy the full SHA
    24c59a7 View commit details
    Browse the repository at this point in the history

Commits on Jun 8, 2023

  1. Add singularity.registry = 'quay.io' and bump NF version to 23.04.0

    @drpatelh
    drpatelh committed Jun 8, 2023
    Configuration menu
    Copy the full SHA
    d1614ff View commit details
    Browse the repository at this point in the history

  2. Update CHANGELOG

    @drpatelh
    drpatelh committed Jun 8, 2023
    Configuration menu
    Copy the full SHA
    00d4fd9 View commit details
    Browse the repository at this point in the history

  3. Fix nf-core lint

    @drpatelh
    drpatelh committed Jun 8, 2023
    Configuration menu
    Copy the full SHA
    8a22c13 View commit details
    Browse the repository at this point in the history

Commits on Jun 9, 2023

  1. Merge branch 'dev' into fix_file_collision_when_using_cellranger

    @adamrtalbot
    adamrtalbot authored Jun 9, 2023
    Configuration menu
    Copy the full SHA
    39b6d49 View commit details
    Browse the repository at this point in the history

  2. revert CI test

    @adamrtalbot
    adamrtalbot committed Jun 9, 2023
    Configuration menu
    Copy the full SHA
    dfa6e49 View commit details
    Browse the repository at this point in the history

Commits on Jun 13, 2023

  1. CHANGELOG

    @adamrtalbot
    adamrtalbot committed Jun 13, 2023
    Configuration menu
    Copy the full SHA
    3fc366e View commit details
    Browse the repository at this point in the history

  2. set CELLRANGER maxForks = 1 when running on test 

    See if this fixes the CI issue
    @adamrtalbot
    adamrtalbot committed Jun 13, 2023
    Configuration menu
    Copy the full SHA
    21666d9 View commit details
    Browse the repository at this point in the history

  3. fixup

    @adamrtalbot
    adamrtalbot committed Jun 13, 2023
    Configuration menu
    Copy the full SHA
    faa1751 View commit details
    Browse the repository at this point in the history

  4. Fix issue with multiqc channel trying to access null objects 

    fixes #231
    @adamrtalbot
    adamrtalbot committed Jun 13, 2023
    Configuration menu
    Copy the full SHA
    a51e4b1 View commit details
    Browse the repository at this point in the history

  5. add explicit channel values to handle multiqc inputs

    @adamrtalbot
    adamrtalbot committed Jun 13, 2023
    Configuration menu
    Copy the full SHA
    db99566 View commit details
    Browse the repository at this point in the history

  6. CHANGELOG

    @adamrtalbot
    adamrtalbot committed Jun 13, 2023
    Configuration menu
    Copy the full SHA
    e6ca31c View commit details
    Browse the repository at this point in the history

  7. Add stub back in because cellranger doesn't work in tests

    @adamrtalbot
    adamrtalbot committed Jun 13, 2023
    Configuration menu
    Copy the full SHA
    02d3c47 View commit details
    Browse the repository at this point in the history

  8. Merge pull request #239 from adamrtalbot/231-null-object-when-running… 

    …-multiqc

fix (231): Null object accessed in multiqc channel
    @adamrtalbot
    adamrtalbot authored Jun 13, 2023
    Configuration menu
    Copy the full SHA
    d745a82 View commit details
    Browse the repository at this point in the history

  9. Merge branch 'dev' into fix_file_collision_when_using_cellranger

    @adamrtalbot
    adamrtalbot authored Jun 13, 2023
    Configuration menu
    Copy the full SHA
    dd6468e View commit details
    Browse the repository at this point in the history

  10. Merge pull request #232 from nf-core/fix_file_collision_when_using_ce… 

    …llranger

Fix_file_collision_when_using_cellranger
    @adamrtalbot
    adamrtalbot authored Jun 13, 2023
    Configuration menu
    Copy the full SHA
    c2034fb View commit details
    Browse the repository at this point in the history

Commits on Jun 14, 2023

  1. Update public_aws_ecr.config

    @maxulysse
    maxulysse authored Jun 14, 2023
    Configuration menu
    Copy the full SHA
    6264efa View commit details
    Browse the repository at this point in the history

  2. Merge pull request #240 from nf-core/maxulysse-patch-1 

    Update public_aws_ecr.config
    @maxulysse
    maxulysse authored Jun 14, 2023
    Configuration menu
    Copy the full SHA
    7d1fb66 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'dev' into quay.io

    @grst
    grst authored Jun 14, 2023
    Configuration menu
    Copy the full SHA
    127eb42 View commit details
    Browse the repository at this point in the history

  4. Merge pull request #237 from drpatelh/quay.io 

    Add singularity.registry = 'quay.io' and bump NF version to 23.04.0
    @grst
    grst authored Jun 14, 2023
    Configuration menu
    Copy the full SHA
    2c1c2a4 View commit details
    Browse the repository at this point in the history

Commits on Jun 19, 2023

  1. Remove public_aws_ecr profile

    @adamrtalbot
    adamrtalbot committed Jun 19, 2023
    Configuration menu
    Copy the full SHA
    0bb02d3 View commit details
    Browse the repository at this point in the history

Commits on Jun 27, 2023

  1. [automated] Fix linting with Prettier

    @nf-core-bot
    nf-core-bot committed Jun 27, 2023
    Configuration menu
    Copy the full SHA
    a70d065 View commit details
    Browse the repository at this point in the history

  2. Reset .devcontainer

    @adamrtalbot
    adamrtalbot committed Jun 27, 2023
    Configuration menu
    Copy the full SHA
    58996c4 View commit details
    Browse the repository at this point in the history

  3. Merge pull request #242 from adamrtalbot/remove-public-aws-ecr-profile 

    Remove public_aws_ecr profile
    @adamrtalbot
    adamrtalbot authored Jun 27, 2023
    Configuration menu
    Copy the full SHA
    a52eb49 View commit details
    Browse the repository at this point in the history

Commits on Jun 29, 2023

  1. Add cellranger to multiqc report

    @grst
    grst committed Jun 29, 2023
    Configuration menu
    Copy the full SHA
    64cb157 View commit details
    Browse the repository at this point in the history

  2. Update CHANGELOG

    @grst
    grst committed Jun 29, 2023
    Configuration menu
    Copy the full SHA
    97dc965 View commit details
    Browse the repository at this point in the history

  3. Initialize with empty channel

    @grst
    grst committed Jun 29, 2023
    Configuration menu
    Copy the full SHA
    3555ef8 View commit details
    Browse the repository at this point in the history

Commits on Jun 30, 2023

  1. Template update for nf-core/tools version 2.9

    @nf-core-bot
    nf-core-bot committed Jun 30, 2023
    Configuration menu
    Copy the full SHA
    bba52df View commit details
    Browse the repository at this point in the history

Commits on Jul 1, 2023

  1. Merge branch 'dev' into nf-core-template-merge-2.9

    @grst
    grst committed Jul 1, 2023
    Configuration menu
    Copy the full SHA
    b466f1b View commit details
    Browse the repository at this point in the history

  2. Remove obsolete multiqc config file

    @grst
    grst committed Jul 1, 2023
    Configuration menu
    Copy the full SHA
    9f1fb75 View commit details
    Browse the repository at this point in the history

  3. Fix linting

    @grst
    grst committed Jul 1, 2023
    Configuration menu
    Copy the full SHA
    0c13d6e View commit details
    Browse the repository at this point in the history

  4. Update modules

    @grst
    grst committed Jul 1, 2023
    Configuration menu
    Copy the full SHA
    d528174 View commit details
    Browse the repository at this point in the history

Commits on Jul 6, 2023

  1. Merge pull request #245 from nf-core/nf-core-template-merge-2.9 

    Important! Template update for nf-core/tools v2.9
    @grst
    grst authored Jul 6, 2023
    Configuration menu
    Copy the full SHA
    f0d5e8e View commit details
    Browse the repository at this point in the history

Commits on Jul 7, 2023

  1. Update usage docs about FASTQ filenames

    @grst
    grst committed Jul 7, 2023
    Configuration menu
    Copy the full SHA
    3b44e56 View commit details
    Browse the repository at this point in the history

  2. Merge pull request #246 from nf-core/update-modules 

    Update cellranger module
    @grst
    grst authored Jul 7, 2023
    Configuration menu
    Copy the full SHA
    0e5fc8b View commit details
    Browse the repository at this point in the history

Commits on Jul 18, 2023

  1. Remove duplicate registry setting from nextflow.config

    @adamrtalbot
    adamrtalbot committed Jul 18, 2023
    Configuration menu
    Copy the full SHA
    1b01084 View commit details
    Browse the repository at this point in the history

Commits on Jul 24, 2023

  1. Merge pull request #252 from adamrtalbot/remove_duplicate_registry_se… 

    …tting

Remove duplicate registry settings in nextflow.config
    @grst
    grst authored Jul 24, 2023
    Configuration menu
    Copy the full SHA
    09da46b View commit details
    Browse the repository at this point in the history

Commits on Aug 7, 2023

  1. Merge branch 'dev' into cellranger-multiqc

    @grst
    grst authored Aug 7, 2023
    Configuration menu
    Copy the full SHA
    66f70ab View commit details
    Browse the repository at this point in the history

  2. Update modules

    @grst
    grst committed Aug 7, 2023
    Configuration menu
    Copy the full SHA
    2771a59 View commit details
    Browse the repository at this point in the history

  3. Fix prettier

    @grst
    grst committed Aug 7, 2023
    Configuration menu
    Copy the full SHA
    8b5707b View commit details
    Browse the repository at this point in the history

Commits on Aug 16, 2023

  1. fix typo causing empty version imformation for mtx_conversion subwork… 

    …flow
    @shinthor
    shinthor committed Aug 16, 2023
    Configuration menu
    Copy the full SHA
    b39bc2d View commit details
    Browse the repository at this point in the history

  2. Merge pull request #244 from grst/cellranger-multiqc 

    Add cellranger to multiqc report
    @grst
    grst authored Aug 16, 2023
    Configuration menu
    Copy the full SHA
    03bf3bf View commit details
    Browse the repository at this point in the history

  3. Fix linting part 1

    @grst
    grst committed Aug 16, 2023
    Configuration menu
    Copy the full SHA
    bfec9ce View commit details
    Browse the repository at this point in the history

  4. Merge branch 'dev' into master

    @grst
    grst authored Aug 16, 2023
    Configuration menu
    Copy the full SHA
    d00b69c View commit details
    Browse the repository at this point in the history

  5. Merge pull request #254 from shinthor/master 

    fix typo causing empty version imformation for mtx_conversion subwork…
    @grst
    grst authored Aug 16, 2023
    Configuration menu
    Copy the full SHA
    21eea72 View commit details
    Browse the repository at this point in the history

  6. Bump version to v2.4.0 for release

    @grst
    grst committed Aug 16, 2023
    Configuration menu
    Copy the full SHA
    d6f2da1 View commit details
    Browse the repository at this point in the history

  7. Update changelog

    @grst
    grst committed Aug 16, 2023
    Configuration menu
    Copy the full SHA
    b302552 View commit details
    Browse the repository at this point in the history

  8. Merge pull request #255 from nf-core/bump-version-for-release 

    Bump version for release
    @grst
    grst authored Aug 16, 2023
    Configuration menu
    Copy the full SHA
    afcb5cf View commit details
    Browse the repository at this point in the history

Commits on Aug 23, 2023

  1. update schema_ignore_params to validationSchemaIgnoreParams

    @maxulysse
    maxulysse committed Aug 23, 2023
    Configuration menu
    Copy the full SHA
    3fdd6f5 View commit details
    Browse the repository at this point in the history

  2. Update conf/test.config

    @maxulysse
    maxulysse authored Aug 23, 2023
    Configuration menu
    Copy the full SHA
    18b26f2 View commit details
    Browse the repository at this point in the history

Commits on Aug 24, 2023

  1. Merge pull request #259 from maxulysse/fix_validation 

    remove validationSchemaIgnoreParams warning with test profile
    @grst
    grst authored Aug 24, 2023
    Configuration menu
    Copy the full SHA
    d2648a4 View commit details
    Browse the repository at this point in the history