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

These updates are awaiting their schedule. Click on a checkbox to get an update now.

• chore(deps): update python:3.12-slim docker digest to 8582432
• chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.11.6

Edited/Blocked

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

• chore(deps): update github actions (codecov/codecov-action, python)
• chore(deps): update dependency textual to v3

Open

These updates have all been created already. Click a checkbox below to force a retry/rebase of any.

• chore(deps): update dependency textual-dev to v1.7.0

Detected dependencies

devcontainer

.devcontainer/devcontainer.json

dockerfile

Dockerfile

• python 3.12-slim@sha256:a866731a6b71c4a194a845d86e06568725e430ed21821d0c52e4efb385cf6c6f

nf_core/gitpod/gitpod.Dockerfile

• gitpod/workspace-base sha256:7f35e401405c38ebc1185dfc3d6c066f73a524e8b86641453ea4690cc5c24fb6

github-actions

.github/actions/create-lint-wf/action.yml

• nf-core/setup-nextflow v2
• actions/upload-artifact v4@ea165f8d65b6e75b540449e92b4886f43607fa02

.github/workflows/branch.yml

• mshick/add-pr-comment v2@b8f338c590a895d50bcbfa6c5859251edc8952fc

.github/workflows/changelog.yml

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-python v5@8d9ed9ac5c53483de85588cdf95a591a75ab9f55
• actions/setup-python v5@8d9ed9ac5c53483de85588cdf95a591a75ab9f55
• python 3.13
• python 3.13

.github/workflows/clean-up.yml

• actions/stale v9@5bef64f19d7facfb25b37b414482c7164d639639

.github/workflows/create-lint-wf.yml

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-python v5@8d9ed9ac5c53483de85588cdf95a591a75ab9f55
• python 3.13

.github/workflows/create-test-lint-wf-template.yml

• frenck/action-setup-yq v1@c4b5be8b4a215c536a41d436757d9feb92836d4f
• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-python v5@8d9ed9ac5c53483de85588cdf95a591a75ab9f55
• nf-core/setup-nextflow v2
• actions/upload-artifact v4@ea165f8d65b6e75b540449e92b4886f43607fa02
• python 3.13

.github/workflows/create-test-wf.yml

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-python v5@8d9ed9ac5c53483de85588cdf95a591a75ab9f55
• nf-core/setup-nextflow v2
• actions/upload-artifact v4@ea165f8d65b6e75b540449e92b4886f43607fa02
• python 3.13

.github/workflows/deploy-pypi.yml

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-python v5@8d9ed9ac5c53483de85588cdf95a591a75ab9f55
• pypa/gh-action-pypi-publish release/v1
• python 3.13

.github/workflows/fix-linting.yml

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• peter-evans/create-or-update-comment v4@71345be0265236311c031f5c7866368bd1eff043
• actions/setup-python v5@8d9ed9ac5c53483de85588cdf95a591a75ab9f55
• peter-evans/create-or-update-comment v4@71345be0265236311c031f5c7866368bd1eff043
• peter-evans/create-or-update-comment v4@71345be0265236311c031f5c7866368bd1eff043
• peter-evans/create-or-update-comment v4@71345be0265236311c031f5c7866368bd1eff043
• peter-evans/create-or-update-comment v4@71345be0265236311c031f5c7866368bd1eff043
• python 3.13

.github/workflows/lint-code.yml

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-python v5@8d9ed9ac5c53483de85588cdf95a591a75ab9f55
• python 3.13

.github/workflows/push_dockerhub_dev.yml

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683

.github/workflows/push_dockerhub_release.yml

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683

.github/workflows/pytest.yml

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-python v5@8d9ed9ac5c53483de85588cdf95a591a75ab9f55
• eWaterCycle/setup-singularity v7@931d4e31109e875b13309ae1d07c70ca8fbc8537
• nf-core/setup-nextflow v2
• nf-core/setup-nf-test v1
• actions/upload-artifact v4@ea165f8d65b6e75b540449e92b4886f43607fa02
• actions/upload-artifact v4@ea165f8d65b6e75b540449e92b4886f43607fa02
• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-python v5@8d9ed9ac5c53483de85588cdf95a591a75ab9f55
• actions/download-artifact v4@95815c38cf2ff2164869cbab79da8d1f422bc89e
• codecov/codecov-action v5@0565863a31f2c772f9f0395002a31e3f06189574
• python 3.13

.github/workflows/sync.yml

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-python v5@8d9ed9ac5c53483de85588cdf95a591a75ab9f55
• nf-core/setup-nextflow v2
• actions/upload-artifact v4@ea165f8d65b6e75b540449e92b4886f43607fa02
• python 3.13

.github/workflows/tools-api-docs.yml

• actions/github-script v7@60a0d83039c74a4aee543508d2ffcb1c3799cdea

.github/workflows/update-textual-snapshots.yml

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• peter-evans/create-or-update-comment v4@71345be0265236311c031f5c7866368bd1eff043
• actions/setup-python v5@8d9ed9ac5c53483de85588cdf95a591a75ab9f55
• peter-evans/create-or-update-comment v4@71345be0265236311c031f5c7866368bd1eff043
• peter-evans/create-or-update-comment v4@71345be0265236311c031f5c7866368bd1eff043
• peter-evans/create-or-update-comment v4@71345be0265236311c031f5c7866368bd1eff043
• peter-evans/create-or-update-comment v4@71345be0265236311c031f5c7866368bd1eff043
• python 3.13

nf_core/pipeline-template/.github/actions/get-shards/action.yml

• nf-core/setup-nf-test v1

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

• nf-core/setup-nextflow v2
• actions/setup-python v5@8d9ed9ac5c53483de85588cdf95a591a75ab9f55
• nf-core/setup-nf-test v1
• eWaterCycle/setup-apptainer main
• conda-incubator/setup-miniconda v3@505e6394dae86d6a5c7fbb6e3fb8938e3e863830
• python 3.11

nf_core/pipeline-template/.github/workflows/awsfulltest.yml

• seqeralabs/action-tower-launch v2
• actions/upload-artifact v4@ea165f8d65b6e75b540449e92b4886f43607fa02

nf_core/pipeline-template/.github/workflows/awstest.yml

• seqeralabs/action-tower-launch v2
• actions/upload-artifact v4@ea165f8d65b6e75b540449e92b4886f43607fa02

nf_core/pipeline-template/.github/workflows/branch.yml

• mshick/add-pr-comment v2@b8f338c590a895d50bcbfa6c5859251edc8952fc

nf_core/pipeline-template/.github/workflows/clean-up.yml

• actions/stale v9@5bef64f19d7facfb25b37b414482c7164d639639

nf_core/pipeline-template/.github/workflows/download_pipeline.yml

• nf-core/setup-nextflow v2
• jlumbroso/free-disk-space v1.3.1@54081f138730dfa15788a46383842cd2f914a1be
• actions/setup-python v5@8d9ed9ac5c53483de85588cdf95a591a75ab9f55
• eWaterCycle/setup-apptainer v2.0.0@4bb22c52d4f63406c49e94c804632975787312b3
• actions/upload-artifact v4@ea165f8d65b6e75b540449e92b4886f43607fa02
• python 3.13

nf_core/pipeline-template/.github/workflows/fix-linting.yml

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• peter-evans/create-or-update-comment v4@71345be0265236311c031f5c7866368bd1eff043
• actions/setup-python v5@8d9ed9ac5c53483de85588cdf95a591a75ab9f55
• peter-evans/create-or-update-comment v4@71345be0265236311c031f5c7866368bd1eff043
• peter-evans/create-or-update-comment v4@71345be0265236311c031f5c7866368bd1eff043
• peter-evans/create-or-update-comment v4@71345be0265236311c031f5c7866368bd1eff043
• peter-evans/create-or-update-comment v4@71345be0265236311c031f5c7866368bd1eff043
• python 3.13

nf_core/pipeline-template/.github/workflows/linting.yml

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-python v5@8d9ed9ac5c53483de85588cdf95a591a75ab9f55
• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• nf-core/setup-nextflow v2
• actions/setup-python v5@8d9ed9ac5c53483de85588cdf95a591a75ab9f55
• pietrobolcato/action-read-yaml 1.1.0@9f13718d61111b69f30ab4ac683e67a56d254e1d
• actions/upload-artifact v4@ea165f8d65b6e75b540449e92b4886f43607fa02
• python 3.13
• python 3.13

nf_core/pipeline-template/.github/workflows/linting_comment.yml

• dawidd6/action-download-artifact v9@07ab29fd4a977ae4d2b275087cf67563dfdf0295
• marocchino/sticky-pull-request-comment v2@52423e01640425a022ef5fd42c6fb5f633a02728

nf_core/pipeline-template/.github/workflows/nf-test.yml

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683

nf_core/pipeline-template/.github/workflows/release-announcements.yml

• rzr/fediverse-action master
• zentered/bluesky-post-action v0.2.0@4aa83560bb3eac05dbad1e5f221ee339118abdd2

nf_core/pipeline-template/.github/workflows/template_version_comment.yml

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• nichmor/minimal-read-yaml v0.0.2@1f7205277e25e156e1f63815781db80a6d490b8f
• mshick/add-pr-comment v2@b8f338c590a895d50bcbfa6c5859251edc8952fc

pep621

pyproject.toml

• setuptools >=40.6.0

pip_requirements

docs/api/requirements.txt

• Sphinx >=3.3.1
• sphinx_rtd_theme >=0.5.0

requirements-dev.txt

• textual-dev ==1.5.1
• typing_extensions >=4.0.0
• pytest-textual-snapshot ==1.1.0
• pytest-workflow >=2.0.0
• pytest >=8.0.0

requirements.txt

• jsonschema >=4.0
• markdown >=3.3
• prompt_toolkit <=3.0.51
• pydantic >=2.2.1
• questionary >=2.0.1
• rich-click ==1.8.*
• rich >=13.3.1
• textual ==2.1.2

pre-commit

.pre-commit-config.yaml

• astral-sh/ruff-pre-commit v0.11.2
• pre-commit/mirrors-prettier v3.1.0
• pre-commit/pre-commit-hooks v5.0.0
• pre-commit/mirrors-mypy v1.15.0

nf_core/pipeline-template/.pre-commit-config.yaml

• pre-commit/mirrors-prettier v3.1.0
• pre-commit/pre-commit-hooks v5.0.0

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