Renovate Dashboard 🤖

[renovate]

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 (16)

[!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	eWaterCycle/setup-apptainer	2025-01-07
github-actions	jlumbroso/free-disk-space	2023-10-18
github-actions	nichmor/minimal-read-yaml	2024-06-05
github-actions	pietrobolcato/action-read-yaml	2023-03-13
pep621	pytest-textual-snapshot	2025-01-23
pep621	pytest-workflow	2024-03-18
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 mcr.microsoft.com/devcontainers/miniconda Docker digest to 1a85cf3
• Update python:3.14-slim Docker digest to 5b3879b
• Update dependency textual to v8.2.4
• Update mcr.microsoft.com/devcontainers/base Docker tag to v2.1.8
• Update pre-commit hooks (astral-sh/ruff-pre-commit, astral-sh/uv-pre-commit, pre-commit/mirrors-mypy)
• 🔐 Create all awaiting schedule PRs at once 🔐

PR Edited (Blocked)

The following updates have been manually edited so Renovate will no longer make changes. To discard all commits and start over, click on a checkbox below.

• Update GitHub Actions (actions/upload-artifact, astral-sh/setup-uv, devcontainers/ci, j178/prek-action, mshick/add-pr-comment, nf-core/setup-nf-test, seqeralabs/action-tower-launch)
• Update dependency prettier to v3.8.3
• Update conda-incubator/setup-miniconda action to v4
• Lock file maintenance

---

Warning

Renovate failed to look up the following dependencies: Could not determine new digest for update (github-tags package marocchino/sticky-pull-request-comment).

Files affected: nf_core/pipeline-template/.github/workflows/linting_comment.yml

---

Other Branches

The following updates are pending. To force the creation of a PR, click on a checkbox below.

• Update dependency pytest to v9 [SECURITY]

Open

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

• Update dependency setuptools to v82

Detected Dependencies

devcontainer (1)

.devcontainer/devcontainer.json

dockerfile (2)

.devcontainer/build-devcontainer/Dockerfile (2)

• mcr.microsoft.com/devcontainers/miniconda sha256:26b252eed80fe93ec85c48b36035098288c3082c78e5b5073b11d69562ee0897 → [Updates: undefined]
• mcr.microsoft.com/devcontainers/base 2.1.7-debian12@sha256:4d49e42a3eda8a8fd8437ecd8830d50a9113dc0f3623226db5e5c10a2b156f1e → [Updates: 2.1.8-debian12]

Dockerfile (1)

• python 3.14-slim@sha256:bc389f7dfcb21413e72a28f491985326994795e34d2b86c8ae2f417b4e7818aa → [Updates: 3.14-slim]

github-actions (31)

.github/actions/create-lint-wf/action.yml (2)

• nf-core/setup-nextflow v3@b4ec1bc7c16a94435159de94a05253542fddf6ef
• actions/upload-artifact v7@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f → [Updates: v7]

.github/workflows/branch.yml (1)

• mshick/add-pr-comment v3@64b8e914979889d746c99dea15a76e77ef64580a → [Updates: v3]

.github/workflows/changelog.yml (7)

• github/branch-deploy v11.1.2@fded0351b6b79f854b335c11b3d93063461dd288
• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• actions/setup-python v6@a309ff8b426b58ec0e2a45f0f869d46889d02405
• actions/setup-python v6@a309ff8b426b58ec0e2a45f0f869d46889d02405
• j178/prek-action v2@53276d8b0d10f8b6672aa85b4588c6921d0370cc → [Updates: v2]
• python 3.14
• python 3.14

.github/workflows/clean-up.yml (1)

• actions/stale v10@b5d41d4e1d5dceea10e7104786b73624c18a190f

.github/workflows/create-lint-wf.yml (4)

• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• actions/setup-python v6@a309ff8b426b58ec0e2a45f0f869d46889d02405
• astral-sh/setup-uv v8.1.0@08807647e7069bb48b6ef5acd8ec9567f424441b
• python 3.14

.github/workflows/create-test-lint-wf-template.yml (8)

• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• actions/setup-python v6@a309ff8b426b58ec0e2a45f0f869d46889d02405
• astral-sh/setup-uv v8.1.0@08807647e7069bb48b6ef5acd8ec9567f424441b
• nf-core/setup-nextflow v3@b4ec1bc7c16a94435159de94a05253542fddf6ef
• nf-core/setup-nf-test v2@ce65500579e8587607aab289ecb3a9c343c32e79 → [Updates: v2]
• actions/upload-artifact v7@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f → [Updates: v7]
• python 3.14

.github/workflows/create-test-wf.yml (7)

• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• actions/setup-python v6@a309ff8b426b58ec0e2a45f0f869d46889d02405
• astral-sh/setup-uv v8.1.0@08807647e7069bb48b6ef5acd8ec9567f424441b
• nf-core/setup-nextflow v3@b4ec1bc7c16a94435159de94a05253542fddf6ef
• nf-core/setup-nf-test v2@ce65500579e8587607aab289ecb3a9c343c32e79 → [Updates: v2]
• actions/upload-artifact v7@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f → [Updates: v7]
• python 3.14

.github/workflows/deploy-pypi.yml (5)

• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• actions/setup-python v6@a309ff8b426b58ec0e2a45f0f869d46889d02405
• astral-sh/setup-uv v8.1.0@08807647e7069bb48b6ef5acd8ec9567f424441b
• pypa/gh-action-pypi-publish release/v1@cef221092ed1bacb1cc03d23a2d87d1d172e277b
• python 3.14

.github/workflows/fix-linting.yml (7)

• github/branch-deploy v11.1.2@fded0351b6b79f854b335c11b3d93063461dd288
• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• j178/prek-action v2@53276d8b0d10f8b6672aa85b4588c6921d0370cc → [Updates: v2]
• 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 v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• j178/prek-action v2@53276d8b0d10f8b6672aa85b4588c6921d0370cc → [Updates: v2]

.github/workflows/nextflow-source-test.yml (7)

• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• actions/setup-java v5@be666c2fcd27ec809703dec50e508c2fdc7f6654
• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• actions/setup-python v6@a309ff8b426b58ec0e2a45f0f869d46889d02405
• astral-sh/setup-uv v8.1.0@08807647e7069bb48b6ef5acd8ec9567f424441b
• dsfx3d/action-aws-ses v1.0.3@a0daa3774d2bb09e2bcb512e55bdc3510b6102ef
• python 3.14

.github/workflows/push_dockerhub.yml (7)

• jlumbroso/free-disk-space main@54081f138730dfa15788a46383842cd2f914a1be
• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• docker/setup-qemu-action v4@ce360397dd3f832beb865e1373c09c0e9f86d70a
• docker/setup-buildx-action v4@4d04d5d9486b7bd6fa91e7baf45bbb4f8b9deedd
• docker/login-action v4@4907a6ddec9925e35a0a9e82d7399ccc52663121
• nick-fields/retry v4@ad984534de44a9489a53aefd81eb77f87c70dc60
• devcontainers/ci v0.3@8bf61b26e9c3a98f69cb6ce2f88d24ff59b785c6 → [Updates: v0.3]

.github/workflows/pytest.yml (9)

• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• actions/setup-python v6@a309ff8b426b58ec0e2a45f0f869d46889d02405
• astral-sh/setup-uv v8.1.0@08807647e7069bb48b6ef5acd8ec9567f424441b
• eWaterCycle/setup-apptainer v2.0.0@4bb22c52d4f63406c49e94c804632975787312b3
• nf-core/setup-nextflow v3@b4ec1bc7c16a94435159de94a05253542fddf6ef
• nf-core/setup-nf-test v2@ce65500579e8587607aab289ecb3a9c343c32e79 → [Updates: v2]
• codecov/codecov-action v6@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2
• actions/upload-artifact v7@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f → [Updates: v7]

.github/workflows/sync.yml (7)

• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• actions/setup-python v6@a309ff8b426b58ec0e2a45f0f869d46889d02405
• astral-sh/setup-uv v8.1.0@08807647e7069bb48b6ef5acd8ec9567f424441b
• nf-core/setup-nextflow v3@b4ec1bc7c16a94435159de94a05253542fddf6ef
• actions/upload-artifact v7@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f → [Updates: v7]
• python 3.14

.github/workflows/test_offline_configs.yml (7)

• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• GuillaumeFalourd/assert-command-line-output v2@2cd32f7751887b5ef1886521de68ea2ec3e2aee7
• GuillaumeFalourd/assert-command-line-output v2@2cd32f7751887b5ef1886521de68ea2ec3e2aee7
• GuillaumeFalourd/assert-command-line-output v2@2cd32f7751887b5ef1886521de68ea2ec3e2aee7
• GuillaumeFalourd/assert-command-line-output v2@2cd32f7751887b5ef1886521de68ea2ec3e2aee7
• 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 v11.1.2@fded0351b6b79f854b335c11b3d93063461dd288
• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• actions/setup-python v6@a309ff8b426b58ec0e2a45f0f869d46889d02405
• astral-sh/setup-uv v8.1.0@08807647e7069bb48b6ef5acd8ec9567f424441b
• nf-core/setup-nextflow v3@b4ec1bc7c16a94435159de94a05253542fddf6ef
• nf-core/setup-nf-test v2@ce65500579e8587607aab289ecb3a9c343c32e79 → [Updates: v2]
• actions/upload-artifact v7@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f → [Updates: v7]
• peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• 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 v11.1.2@fded0351b6b79f854b335c11b3d93063461dd288
• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
• actions/setup-python v6@a309ff8b426b58ec0e2a45f0f869d46889d02405
• astral-sh/setup-uv v8.1.0@08807647e7069bb48b6ef5acd8ec9567f424441b
• 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@ce65500579e8587607aab289ecb3a9c343c32e79 → [Updates: v2]

nf_core/pipeline-template/.github/actions/nf-test/action.yml (6)

• nf-core/setup-nextflow v3@b4ec1bc7c16a94435159de94a05253542fddf6ef
• actions/setup-python v6@a309ff8b426b58ec0e2a45f0f869d46889d02405
• nf-core/setup-nf-test v2@ce65500579e8587607aab289ecb3a9c343c32e79 → [Updates: v2]
• eWaterCycle/setup-apptainer v2@3f706d898c9db585b1d741b4692e66755f3a1b40
• conda-incubator/setup-miniconda v3@fc2d68f6413eb2d87b895e92f8584b5b94a10167 → [Updates: v4]
• python 3.14

nf_core/pipeline-template/.github/workflows/awsfulltest.yml (2)

• seqeralabs/action-tower-launch v2 → [Updates: v2]
• actions/upload-artifact v7@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f → [Updates: v7]

nf_core/pipeline-template/.github/workflows/awstest.yml (2)

• seqeralabs/action-tower-launch v2 → [Updates: v2]
• actions/upload-artifact v7@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f → [Updates: v7]

nf_core/pipeline-template/.github/workflows/branch.yml (1)

• mshick/add-pr-comment v3@64b8e914979889d746c99dea15a76e77ef64580a → [Updates: v3]

nf_core/pipeline-template/.github/workflows/clean-up.yml (1)

• actions/stale v10@b5d41d4e1d5dceea10e7104786b73624c18a190f

nf_core/pipeline-template/.github/workflows/download_pipeline.yml (7)

• nf-core/setup-nextflow v3@b4ec1bc7c16a94435159de94a05253542fddf6ef
• jlumbroso/free-disk-space v1.3.1@54081f138730dfa15788a46383842cd2f914a1be
• actions/setup-python v6@a309ff8b426b58ec0e2a45f0f869d46889d02405
• eWaterCycle/setup-apptainer v2.0.0@4bb22c52d4f63406c49e94c804632975787312b3
• pietrobolcato/action-read-yaml 1.1.0@9f13718d61111b69f30ab4ac683e67a56d254e1d
• actions/upload-artifact v7@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f → [Updates: v7]
• python 3.14

nf_core/pipeline-template/.github/workflows/fix_linting.yml (7)

• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
• j178/prek-action v2@53276d8b0d10f8b6672aa85b4588c6921d0370cc → [Updates: v2]
• 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_comment.yml (2)

• dawidd6/action-download-artifact v20@8305c0f1062bb0d184d09ef4493ecb9288447732
• marocchino/sticky-pull-request-comment v3@70d2764d1a7d5d9560b100cbea0077fc8f633987

nf_core/pipeline-template/.github/workflows/linting.yml (9)

• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• j178/prek-action v2@53276d8b0d10f8b6672aa85b4588c6921d0370cc → [Updates: v2]
• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• nf-core/setup-nextflow v3@b4ec1bc7c16a94435159de94a05253542fddf6ef
• actions/setup-python v6@a309ff8b426b58ec0e2a45f0f869d46889d02405
• astral-sh/setup-uv v8.0.0@cec208311dfd045dd5311c1add060b2062131d57 → [Updates: v8.1.0]
• pietrobolcato/action-read-yaml 1.1.0@9f13718d61111b69f30ab4ac683e67a56d254e1d
• actions/upload-artifact v7@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f → [Updates: v7]
• python 3.14

nf_core/pipeline-template/.github/workflows/nf-test.yml (2)

• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd

nf_core/pipeline-template/.github/workflows/release-announcements.yml (2)

• rzr/fediverse-action master@563159eb8d45f70ab6aaba36ed55cd037e51f441
• zentered/bluesky-post-action v0.4.0@5a91cc2ad10a304a4e96c16182dbe4918710bcf6

nf_core/pipeline-template/.github/workflows/template-version-comment.yml (3)

• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• nichmor/minimal-read-yaml v0.0.2@1f7205277e25e156e1f63815781db80a6d490b8f
• mshick/add-pr-comment v3@64b8e914979889d746c99dea15a76e77ef64580a → [Updates: v3]

pep621 (1)

pyproject.toml (17)

• 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 <81 → [Updates: <83]
• textual ==8.2.3 → [Updates: ==8.2.4]
• textual-dev ==1.8.0
• typing-extensions >=4.0.0
• 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 v0.15.11 → [Updates: v0.15.12]
• pre-commit/mirrors-prettier v3.1.0
• pre-commit/pre-commit-hooks v6.0.0
• pre-commit/mirrors-mypy v1.20.0 → [Updates: v1.20.2]
• astral-sh/uv-pre-commit 0.11.4 → [Updates: 0.11.7]

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 3.8.1 → [Updates: 3.8.3]

nf_core/.pre-commit-prettier-config.yaml (1)

• prettier 3.8.1 → [Updates: 3.8.3]

nf_core/pipeline-template/.pre-commit-config.yaml (1)

• prettier 3.8.1 → [Updates: 3.8.3]

renovate-config-presets (1)

.github/renovate.json5

---

• Check this box to trigger a request for Renovate to run again on this repository