Renovate Dashboard 🤖

[renovate]

This issue lists Renovate updates and detected dependencies. Read the Dependency Dashboard docs to learn more.
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Abandoned Dependencies

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

View abandoned dependencies (21)

[!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

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 a7fb1e6

Open

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

• Update dependency pytest to v9 [SECURITY]
• Update mcr.microsoft.com/devcontainers/miniconda Docker digest to 26f4e9d
• Update GitHub Actions (CodSpeedHQ/action, actions/setup-java, eWaterCycle/setup-apptainer, pypa/gh-action-pypi-publish)
• Update mcr.microsoft.com/devcontainers/base Docker tag to v2.1.13
• Update pre-commit hooks (astral-sh/ruff-pre-commit, astral-sh/uv-pre-commit)
• Update j178/prek-action action to v3
• Lock file maintenance
• Click on this checkbox to rebase all open PRs at once

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
• 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
• 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
• 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
• 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
• 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
• dsfx3d/action-aws-ses v1.0.3@a0daa3774d2bb09e2bcb512e55bdc3510b6102ef
• python 3.14

.github/workflows/pr-comment.yml (2)

• dawidd6/action-download-artifact v21@b6e2e70617bc3265edd6dab6c906732b2f1ae151
• 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
• 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
• 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
• 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
• 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
• 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
• 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: v0.16.2]
• pre-commit/mirrors-prettier v3.1.0
• pre-commit/pre-commit-hooks v6.0.0
• pre-commit/mirrors-mypy v2.3.0
• astral-sh/uv-pre-commit 0.12.0 → [Updates: 0.12.3]

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

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