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[renovate]

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

Awaiting Schedule

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

• Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.2

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.

• Update conda-incubator/setup-miniconda digest to d2e6a04

Open

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

• Update dependency textual to v0.85.2

Detected dependencies

devcontainer

.devcontainer/devcontainer.json

dockerfile

Dockerfile

• python 3.12-slim@sha256:032c52613401895aa3d418a4c563d2d05f993bc3ecc065c8f4e2280978acd249

nf_core/gitpod/gitpod.Dockerfile

• gitpod/workspace-base sha256:2cc134fe5bd7d8fdbe44cab294925d4bc6d2d178d94624f4c376584a22d1f7b6

github-actions

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

• nf-core/setup-nextflow v2
• actions/upload-artifact v4@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882

.github/workflows/branch.yml

• mshick/add-pr-comment v2@b8f338c590a895d50bcbfa6c5859251edc8952fc

.github/workflows/changelog.yml

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-python v5@0b93645e9fea7318ecaed2b359559ac225c90a2b
• actions/setup-python v5@0b93645e9fea7318ecaed2b359559ac225c90a2b

.github/workflows/clean-up.yml

• actions/stale v9@28ca1036281a5e5922ead5184a1bbf96e5fc984e

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

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-python v5@0b93645e9fea7318ecaed2b359559ac225c90a2b

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

• frenck/action-setup-yq v1
• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-python v5@0b93645e9fea7318ecaed2b359559ac225c90a2b
• nf-core/setup-nextflow v2
• actions/upload-artifact v4@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882

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

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-python v5@0b93645e9fea7318ecaed2b359559ac225c90a2b
• nf-core/setup-nextflow v2
• actions/upload-artifact v4@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882

.github/workflows/deploy-pypi.yml

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-python v5@0b93645e9fea7318ecaed2b359559ac225c90a2b
• pypa/gh-action-pypi-publish release/v1

.github/workflows/fix-linting.yml

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• peter-evans/create-or-update-comment v4@71345be0265236311c031f5c7866368bd1eff043
• actions/setup-python v5@0b93645e9fea7318ecaed2b359559ac225c90a2b
• 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

.github/workflows/lint-code.yml

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-python v5@0b93645e9fea7318ecaed2b359559ac225c90a2b

.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@0b93645e9fea7318ecaed2b359559ac225c90a2b
• eWaterCycle/setup-singularity v7@931d4e31109e875b13309ae1d07c70ca8fbc8537
• nf-core/setup-nextflow v2
• nf-core/setup-nf-test v1
• actions/upload-artifact v4@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882
• actions/upload-artifact v4@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882
• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-python v5@0b93645e9fea7318ecaed2b359559ac225c90a2b
• actions/download-artifact v4@fa0a91b85d4f404e444e00e005971372dc801d16
• codecov/codecov-action v4@b9fd7d16f6d7d1b5d2bec1a2887e65ceed900238

.github/workflows/sync.yml

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-python v5@0b93645e9fea7318ecaed2b359559ac225c90a2b
• nf-core/setup-nextflow v2
• actions/upload-artifact v4@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882

.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@0b93645e9fea7318ecaed2b359559ac225c90a2b
• 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

.github/workflows/update_components_template.yml

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-python v5@0b93645e9fea7318ecaed2b359559ac225c90a2b

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

• octokit/request-action v2.x
• seqeralabs/action-tower-launch v2
• actions/upload-artifact v4

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

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

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

• mshick/add-pr-comment v2@b8f338c590a895d50bcbfa6c5859251edc8952fc

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

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• nf-core/setup-nextflow v2
• eWaterCycle/setup-apptainer main
• conda-incubator/setup-miniconda v3@a4260408e20b96e80095f42ff7f1a15b27dd94ca
• jlumbroso/free-disk-space v1.3.1@54081f138730dfa15788a46383842cd2f914a1be

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

• actions/stale v9@28ca1036281a5e5922ead5184a1bbf96e5fc984e

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@0b93645e9fea7318ecaed2b359559ac225c90a2b
• eWaterCycle/setup-apptainer v2.0.0@4bb22c52d4f63406c49e94c804632975787312b3

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@0b93645e9fea7318ecaed2b359559ac225c90a2b
• 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

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

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-python v5@0b93645e9fea7318ecaed2b359559ac225c90a2b
• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• nf-core/setup-nextflow v2
• actions/setup-python v5@0b93645e9fea7318ecaed2b359559ac225c90a2b
• pietrobolcato/action-read-yaml 1.1.0
• actions/upload-artifact v4@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882

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

• dawidd6/action-download-artifact v6@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11
• marocchino/sticky-pull-request-comment v2@331f8f5b4215f0445d3c07b4967662a32a2d3e31

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

• rzr/fediverse-action master
• actions/setup-python v5@0b93645e9fea7318ecaed2b359559ac225c90a2b
• zentered/bluesky-post-action v0.1.0@80dbe0a7697de18c15ad22f4619919ceb5ccf597

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

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• nichmor/minimal-read-yaml v0.0.2
• 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 ==1.6.1
• typing_extensions >=4.0.0
• pytest-textual-snapshot ==1.0.0
• pytest-workflow >=2.0.0
• pytest >=8.0.0

requirements.txt

• jsonschema >=4.0
• markdown >=3.3
• prompt_toolkit <=3.0.48
• pydantic >=2.2.1
• questionary >=2.0.1
• rich-click ==1.8.*
• rich >=13.3.1
• textual ==0.71.0

pre-commit

.pre-commit-config.yaml

• astral-sh/ruff-pre-commit v0.7.1
• pre-commit/mirrors-prettier v3.1.0
• editorconfig-checker/editorconfig-checker.python 3.0.3
• pre-commit/mirrors-mypy v1.13.0

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

• pre-commit/mirrors-prettier v3.1.0
• editorconfig-checker/editorconfig-checker.python 3.0.3

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