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Bump Parabricks to version 4.7.1 - #1899

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gburnett-nvidia wants to merge 2 commits into
nf-core:devfrom
gburnett-nvidia:bump-parabricks-star-version
Open

Bump Parabricks to version 4.7.1#1899
gburnett-nvidia wants to merge 2 commits into
nf-core:devfrom
gburnett-nvidia:bump-parabricks-star-version

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@gburnett-nvidia

@gburnett-nvidia gburnett-nvidia commented Jul 31, 2026 •
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This newer Parabricks version offers performance improvements for rna_fq2bam (STAR).

See release notes for 4.7 and 4.7.1 for more information.

@github-actions

github-actions Bot commented Jul 31, 2026

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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @gburnett-nvidia,

It looks like this pull-request is has been made against the gburnett-nvidia/rnaseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the gburnett-nvidia/rnaseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@gburnett-nvidia
gburnett-nvidia changed the base branch from master to dev July 31, 2026 20:08
@github-actions

github-actions Bot commented Jul 31, 2026

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.3.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

@github-actions

github-actions Bot commented Jul 31, 2026 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 635e8ed

+| ✅ 213 tests passed       |+
#| ❔  22 tests were ignored |#
!| ❗   8 tests had warnings |!
-| ❌   3 tests failed       |-
Details

❌ Test failures:

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/rnaseq/rnaseq/lint_results.md: _* pipeline_if_empty_null - No ifEmpty(null) strings found
    _

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: conf/containers_conda_lock_files_amd64.config
  • files_exist - File is ignored: conf/containers_conda_lock_files_arm64.config
  • files_exist - File is ignored: conf/containers_docker_amd64.config
  • files_exist - File is ignored: conf/containers_docker_arm64.config
  • files_exist - File is ignored: conf/containers_singularity_https_amd64.config
  • files_exist - File is ignored: conf/containers_singularity_https_arm64.config
  • files_exist - File is ignored: conf/containers_singularity_oras_amd64.config
  • files_exist - File is ignored: conf/containers_singularity_oras_arm64.config
  • files_exist - File is ignored: .github/workflows/linting_comment.yml
  • nextflow_config - Config default ignored: params.ribo_database_manifest
  • nf_test_content - nf_test_content
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: assets/nf-core-rnaseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-rnaseq_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_nf_test - actions_nf_test
  • modules_config - modules_config
  • container_configs - container_configs

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.3
  • Run at 2026-07-31 20:13:53

@gburnett-nvidia

gburnett-nvidia commented Jul 31, 2026

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@nf-core-bot fix linting

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