nf-core / nf-core/tools

Renovate Dashboard 🤖

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Merged PRs (30d)
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Description

This issue lists Renovate updates and detected dependencies. Read the Dependency Dashboard docs to learn more.
View this repository on the Mend.io Web Portal.

Abandoned Dependencies

The following dependencies have not received updates for an extended period and may be unmaintained.

View abandoned dependencies (23)

[!NOTE]
Packages are marked as abandoned when they exceed the abandonmentThreshold since their last release. Unlike deprecated packages with official notices, abandonment is detected by release inactivity.

Datasource Package Last Updated
github-actions GuillaumeFalourd/assert-command-line-output 2024-09-20
github-actions dsfx3d/action-aws-ses 2025-05-29
github-actions eWaterCycle/setup-apptainer 2025-01-07
github-actions jlumbroso/free-disk-space 2023-10-27
github-actions nichmor/minimal-read-yaml 2024-06-05
github-actions pietrobolcato/action-read-yaml 2023-03-13
github-actions rzr/fediverse-action 2020-03-15
github-actions seqeralabs/action-tower-launch 2025-06-25
pep621 pytest-clarity 2021-06-11
pep621 pytest-textual-snapshot 2025-01-23
pep621 pytest-workflow 2024-03-18
pep621 pytest-xdist 2025-07-01
pre-commit pre-commit/mirrors-prettier 2023-12-21
pre-commit pre-commit/pre-commit-hooks 2025-08-09

Awaiting Schedule

The following updates are awaiting their schedule. To get an update now, click on a checkbox below.

  • Update python:3.14-slim Docker digest to ce40764

Open

The following updates have all been created. To force a retry/rebase of any, click on a checkbox below.

Detected Dependencies

devcontainer (1)
.devcontainer/devcontainer.json
dockerfile (2)
.devcontainer/build-devcontainer/Dockerfile (2)
  • mcr.microsoft.com/devcontainers/miniconda sha256:617c7e42311066ac0bac3b7f0a3647daa9eec70fb8e3aeb8a5b083337a8a8687 → [Updates: undefined]
  • mcr.microsoft.com/devcontainers/base 2.1.11-debian12@sha256:bb7b81b6e5be17b5267f92f4ffda534fea37dab1df97b5e86c1f9b91da5c0b5d → [Updates: 2.1.13-debian12]
Dockerfile (1)
  • python 3.14-slim@sha256:cea0e6040540fb2b965b6e7fb5ffa00871e632eef63719f0ea54bca189ce14a6 → [Updates: 3.14-slim]
github-actions (33)
.github/actions/create-lint-wf/action.yml (2)
  • nf-core/setup-nextflow v3@893c28b667aedeba26e37f296d260ccc5bc4d914
  • actions/upload-artifact v7@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
.github/workflows/branch.yml (1)
  • actions/upload-artifact v7@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
.github/workflows/changelog.yml (6)
  • actions/checkout v7.0.1@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/setup-python v7@5fda3b95a4ea91299a34e894583c3862153e4b97
  • actions/setup-python v7@5fda3b95a4ea91299a34e894583c3862153e4b97
  • j178/prek-action v2@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 → [Updates: v3.0.0]
  • python 3.14
  • python 3.14
.github/workflows/clean-up.yml (1)
  • actions/stale v11@4391f3da665fdf50b6810c1a66712fb9ba21aa93
.github/workflows/codspeed.yml (6)
  • actions/checkout v7.0.1@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/setup-python v7@5fda3b95a4ea91299a34e894583c3862153e4b97
  • nf-core/setup-nextflow v3@893c28b667aedeba26e37f296d260ccc5bc4d914
  • astral-sh/setup-uv v9.0.0@c771a70e6277c0a99b617c7a806ffedaca235ff9 → [Updates: v10.0.1]
  • CodSpeedHQ/action v5.0.1@88472375d0a4572cf70a9f1fe3a4e0ab8da1b924 → [Updates: v5.0.3]
  • python 3.14
.github/workflows/create-lint-wf.yml (4)
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/setup-python v7@5fda3b95a4ea91299a34e894583c3862153e4b97
  • astral-sh/setup-uv v9.0.0@c771a70e6277c0a99b617c7a806ffedaca235ff9 → [Updates: v10.0.1]
  • python 3.14
.github/workflows/create-test-lint-wf-template.yml (8)
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/setup-python v7@5fda3b95a4ea91299a34e894583c3862153e4b97
  • astral-sh/setup-uv v9.0.0@c771a70e6277c0a99b617c7a806ffedaca235ff9 → [Updates: v10.0.1]
  • nf-core/setup-nextflow v3@893c28b667aedeba26e37f296d260ccc5bc4d914
  • nf-core/setup-nf-test v2@4069fbbaabe94c08faba4ad261bfa88225ba133f
  • actions/upload-artifact v7@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
  • python 3.14
.github/workflows/create-test-wf.yml (7)
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/setup-python v7@5fda3b95a4ea91299a34e894583c3862153e4b97
  • astral-sh/setup-uv v9.0.0@c771a70e6277c0a99b617c7a806ffedaca235ff9 → [Updates: v10.0.1]
  • nf-core/setup-nextflow v3@893c28b667aedeba26e37f296d260ccc5bc4d914
  • nf-core/setup-nf-test v2@4069fbbaabe94c08faba4ad261bfa88225ba133f
  • actions/upload-artifact v7@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
  • python 3.14
.github/workflows/deploy-pypi.yml (5)
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/setup-python v7@5fda3b95a4ea91299a34e894583c3862153e4b97
  • astral-sh/setup-uv v9.0.0@c771a70e6277c0a99b617c7a806ffedaca235ff9 → [Updates: v10.0.1]
  • pypa/gh-action-pypi-publish release/v1@ba38be9e461d3875417946c167d0b5f3d385a247 → [Updates: release/v1]
  • python 3.14
.github/workflows/fix-linting.yml (7)
  • github/branch-deploy v12.0.0@f0984057ffe1aa340aa017b6eafb894310aed88e
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • j178/prek-action v2@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 → [Updates: v3.0.0]
  • peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
  • peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
  • peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
  • peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
.github/workflows/lint-code.yml (2)
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • j178/prek-action v2@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 → [Updates: v3.0.0]
.github/workflows/nextflow-source-test.yml (7)
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/setup-java v5@03ad4de0992f5dab5e18fcb136590ce7c4a0ac95 → [Updates: v5]
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/setup-python v7@5fda3b95a4ea91299a34e894583c3862153e4b97
  • astral-sh/setup-uv v9.0.0@c771a70e6277c0a99b617c7a806ffedaca235ff9 → [Updates: v10.0.1]
  • dsfx3d/action-aws-ses v1.0.3@a0daa3774d2bb09e2bcb512e55bdc3510b6102ef
  • python 3.14
.github/workflows/pr-comment.yml (2)
  • dawidd6/action-download-artifact v21@b6e2e70617bc3265edd6dab6c906732b2f1ae151 → [Updates: v23]
  • marocchino/sticky-pull-request-comment v3.0.5@5770ad5eb8f42dd2c4f34da00c94c5381e49af88
.github/workflows/push_dockerhub.yml (7)
  • jlumbroso/free-disk-space main@54081f138730dfa15788a46383842cd2f914a1be
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • docker/setup-qemu-action v4@96fe6ef7f33517b61c61be40b68a1882f3264fb8
  • docker/setup-buildx-action v4@bb05f3f5519dd87d3ba754cc423b652a5edd6d2c
  • docker/login-action v4@dbcb813823bdd20940b903addbd779551569679f
  • nick-fields/retry v4@ad984534de44a9489a53aefd81eb77f87c70dc60
  • devcontainers/ci v0.3@513af61f4de4f75d37e4438f184ba4358f0fc1ca
.github/workflows/pytest.yml (9)
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/setup-python v7@5fda3b95a4ea91299a34e894583c3862153e4b97
  • astral-sh/setup-uv v9.0.0@c771a70e6277c0a99b617c7a806ffedaca235ff9 → [Updates: v10.0.1]
  • eWaterCycle/setup-apptainer v2.0.0@4bb22c52d4f63406c49e94c804632975787312b3
  • nf-core/setup-nextflow v3@893c28b667aedeba26e37f296d260ccc5bc4d914
  • nf-core/setup-nf-test v2@4069fbbaabe94c08faba4ad261bfa88225ba133f
  • codecov/codecov-action v7@fb8b3582c8e4def4969c97caa2f19720cb33a72f
  • actions/upload-artifact v7@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
.github/workflows/sync.yml (8)
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/setup-python v7@5fda3b95a4ea91299a34e894583c3862153e4b97
  • astral-sh/setup-uv v9.0.0@c771a70e6277c0a99b617c7a806ffedaca235ff9 → [Updates: v10.0.1]
  • nf-core/setup-nextflow v3@893c28b667aedeba26e37f296d260ccc5bc4d914
  • nf-core/setup-nextflow v3@893c28b667aedeba26e37f296d260ccc5bc4d914
  • actions/upload-artifact v7@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
  • python 3.14
.github/workflows/test_offline_configs.yml (7)
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • GuillaumeFalourd/assert-command-line-output v2.4@63ad23408d758ee7f09b4557cc0901d6ae4f3f76
  • GuillaumeFalourd/assert-command-line-output v2.4@63ad23408d758ee7f09b4557cc0901d6ae4f3f76
  • GuillaumeFalourd/assert-command-line-output v2.4@63ad23408d758ee7f09b4557cc0901d6ae4f3f76
  • GuillaumeFalourd/assert-command-line-output v2.4@63ad23408d758ee7f09b4557cc0901d6ae4f3f76
  • actions/github-script v9@3a2844b7e9c422d3c10d287c895573f7108da1b3
.github/workflows/tools-api-docs.yml (1)
  • actions/github-script v9@3a2844b7e9c422d3c10d287c895573f7108da1b3
.github/workflows/update-template-snapshots.yml (15)
  • github/branch-deploy v12.0.0@f0984057ffe1aa340aa017b6eafb894310aed88e
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/setup-python v7@5fda3b95a4ea91299a34e894583c3862153e4b97
  • astral-sh/setup-uv v9.0.0@c771a70e6277c0a99b617c7a806ffedaca235ff9 → [Updates: v10.0.1]
  • nf-core/setup-nextflow v3@893c28b667aedeba26e37f296d260ccc5bc4d914
  • nf-core/setup-nf-test v2@4069fbbaabe94c08faba4ad261bfa88225ba133f
  • actions/upload-artifact v7@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
  • peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/download-artifact v8@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c
  • peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
  • peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
  • peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
  • python 3.14
.github/workflows/update-textual-snapshots.yml (10)
  • github/branch-deploy v12.0.0@f0984057ffe1aa340aa017b6eafb894310aed88e
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
  • actions/setup-python v7@5fda3b95a4ea91299a34e894583c3862153e4b97
  • astral-sh/setup-uv v9.0.0@c771a70e6277c0a99b617c7a806ffedaca235ff9 → [Updates: v10.0.1]
  • peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
  • peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
  • peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
  • peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
  • python 3.14
nf_core/pipeline-template/.github/actions/get-shards/action.yml (1)
  • nf-core/setup-nf-test v2@4069fbbaabe94c08faba4ad261bfa88225ba133f
nf_core/pipeline-template/.github/actions/nf-test/action.yml (6)
  • nf-core/setup-nextflow v3@893c28b667aedeba26e37f296d260ccc5bc4d914
  • actions/setup-python v7@5fda3b95a4ea91299a34e894583c3862153e4b97
  • nf-core/setup-nf-test v2@4069fbbaabe94c08faba4ad261bfa88225ba133f
  • eWaterCycle/setup-apptainer v2.0.0@3f706d898c9db585b1d741b4692e66755f3a1b40 → [Updates: v2.0.0]
  • conda-incubator/setup-miniconda v4@8ee1f361103df19b6f8c8655fd3967a8ecb162d5
  • python 3.14
nf_core/pipeline-template/.github/workflows/awsfulltest.yml (2)
  • seqeralabs/action-tower-launch v2@51565b514bff1827cf34620de25d0055759f1fc9
  • actions/upload-artifact v7@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
nf_core/pipeline-template/.github/workflows/awstest.yml (2)
  • seqeralabs/action-tower-launch v2@51565b514bff1827cf34620de25d0055759f1fc9
  • actions/upload-artifact v7@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
nf_core/pipeline-template/.github/workflows/branch.yml (1)
  • actions/upload-artifact v7@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
nf_core/pipeline-template/.github/workflows/clean-up.yml (1)
  • actions/stale v11@4391f3da665fdf50b6810c1a66712fb9ba21aa93
nf_core/pipeline-template/.github/workflows/download_pipeline.yml (7)
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • nf-core/setup-nextflow v3@893c28b667aedeba26e37f296d260ccc5bc4d914
  • jlumbroso/free-disk-space v1.3.1@54081f138730dfa15788a46383842cd2f914a1be
  • actions/setup-python v7@5fda3b95a4ea91299a34e894583c3862153e4b97
  • eWaterCycle/setup-apptainer v2.0.0@4bb22c52d4f63406c49e94c804632975787312b3
  • actions/upload-artifact v7@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
  • python 3.14
nf_core/pipeline-template/.github/workflows/fix_linting.yml (8)
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
  • nf-core/setup-nextflow v3@893c28b667aedeba26e37f296d260ccc5bc4d914
  • j178/prek-action v2@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 → [Updates: v3.0.0]
  • peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
  • peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
  • peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
  • peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
nf_core/pipeline-template/.github/workflows/linting.yml (11)
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • nf-core/setup-nextflow v3@893c28b667aedeba26e37f296d260ccc5bc4d914
  • j178/prek-action v2@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 → [Updates: v3.0.0]
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • nf-core/setup-nextflow v3@893c28b667aedeba26e37f296d260ccc5bc4d914
  • actions/setup-python v7@5fda3b95a4ea91299a34e894583c3862153e4b97
  • astral-sh/setup-uv v9.0.0@c771a70e6277c0a99b617c7a806ffedaca235ff9 → [Updates: v10.0.1]
  • pietrobolcato/action-read-yaml 1.1.0@9f13718d61111b69f30ab4ac683e67a56d254e1d
  • actions/upload-artifact v7@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
  • actions/upload-artifact v7@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
  • python 3.14
nf_core/pipeline-template/.github/workflows/nf-test.yml (5)
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/upload-artifact v7@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
  • actions/download-artifact v8.0.1@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c
  • actions/upload-artifact v7@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
nf_core/pipeline-template/.github/workflows/pr-comment.yml (2)
  • dawidd6/action-download-artifact v21@b6e2e70617bc3265edd6dab6c906732b2f1ae151 → [Updates: v23]
  • marocchino/sticky-pull-request-comment v3.0.5@5770ad5eb8f42dd2c4f34da00c94c5381e49af88
nf_core/pipeline-template/.github/workflows/release-announcements.yml (2)
  • rzr/fediverse-action v0.0.6@66c2cbb5b1997666b0e28d597631b6a4f09a2719
  • zentered/bluesky-post-action v0.4.0@5a91cc2ad10a304a4e96c16182dbe4918710bcf6
nf_core/pipeline-template/.github/workflows/template-version-comment.yml (3)
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • nichmor/minimal-read-yaml v0.0.2@1f7205277e25e156e1f63815781db80a6d490b8f
  • actions/upload-artifact v7@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
pep621 (1)
pyproject.toml (21)
  • python >=3.10, <4
  • jsonschema >=4.0
  • markdown >=3.3
  • prompt_toolkit <=3.0.52
  • pydantic >=2.2.1
  • questionary >=2.0.1
  • rich-click ==1.9.*
  • rich >=13.3.1
  • setuptools <84
  • textual ==8.2.8
  • mypy >=2.0.0
  • textual-dev ==1.8.0
  • typing-extensions >=4.0.0
  • pytest-clarity >=1.0.1
  • pytest-codspeed >=5.0.3
  • pytest-sugar >=1.1.1
  • pytest-textual-snapshot ==1.1.0
  • pytest-workflow >=2.0.0
  • pytest-xdist >=3.7.0
  • pytest >=8.0.0 → [Updates: >=8.0.0]
  • setuptools >=40.6.0
pip_requirements (1)
docs/api/requirements.txt (2)
  • Sphinx >=3.3.1
  • sphinx_rtd_theme >=0.5.0
pre-commit (2)
.pre-commit-config.yaml (5)
  • astral-sh/ruff-pre-commit v0.16.0 → [Updates: v0.16.3]
  • pre-commit/mirrors-prettier v3.1.0
  • pre-commit/pre-commit-hooks v6.0.0
  • pre-commit/mirrors-mypy v2.3.0 → [Updates: v2.3.1]
  • astral-sh/uv-pre-commit 0.12.0 → [Updates: 0.12.5]
nf_core/pipeline-template/.pre-commit-config.yaml (3)
  • pre-commit/mirrors-prettier v3.1.0
  • pre-commit/pre-commit-hooks v6.0.0
  • seqeralabs/nf-lint-pre-commit v0.3.0
regex (3)
.pre-commit-config.yaml (1)
  • prettier 3.9.6
nf_core/.pre-commit-prettier-config.yaml (1)
  • prettier 3.9.6
nf_core/pipeline-template/.pre-commit-config.yaml (1)
  • prettier 3.9.6
renovate-config (1)
.github/renovate.json5
  • Check this box to trigger a request for Renovate to run again on this repository

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the Renovate dashboard entries and their linked pull requests, then inspect the listed files such as .devcontainer/build-devcontainer/Dockerfile, Dockerfile, and the .github/workflows files. Review which dependency updates remain relevant and verify the corresponding CI and container checks; done means the applicable updates are handled or the dashboard is no longer actionable.

Written by the indexing model from the issue text.

Assessment

Tech stack
docker, github-actions, python
Domain
build-system, ci-cd, devops
Issue type
Refactor
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
15/100

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