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[renovate]

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

Repository problems

These problems occurred while renovating this repository. View logs.

• WARN: Found renovate config warnings
• WARN: Package lookup failures

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Warning

Renovate failed to look up the following dependencies: Could not determine new digest for update (docker package ghcr.io/devcontainers/features/github-cli), Could not determine new digest for update (docker package ghcr.io/devcontainers/features/docker-in-docker), Failed to look up docker package docker/dockerfile, Failed to look up docker package continuumio/miniconda3, Failed to look up docker package tensorflow/tensorflow, Failed to look up docker package nfcore/base, Failed to look up docker package ubuntu.

Files affected: .devcontainer/devcontainer.json, modules/nf-core/bclconvert/Dockerfile, modules/nf-core/cellranger/mkfastq/Dockerfile, modules/nf-core/cellrangerarc/Dockerfile, modules/nf-core/cellrangerarc/mkfastq/Dockerfile, modules/nf-core/cellrangeratac/Dockerfile, modules/nf-core/cellrangeratac/mkfastq/Dockerfile, modules/nf-core/coreograph/Dockerfile, modules/nf-core/ensemblvep/Dockerfile, modules/nf-core/quartonotebook/Dockerfile, modules/nf-core/snpeff/Dockerfile, modules/nf-core/spaceranger/Dockerfile, modules/nf-core/xeniumranger/Dockerfile

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Open

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

• chore(deps): update condaforge/mambaforge:24.1.2-0 docker digest to 5e370da
• chore(deps): update dotnet monorepo (mcr.microsoft.com/dotnet/runtime, mcr.microsoft.com/dotnet/sdk)
• chore(deps): update condaforge/mambaforge docker tag to v24.9.0
• chore(deps): update dotnet monorepo to v9 (major) (mcr.microsoft.com/dotnet/runtime, mcr.microsoft.com/dotnet/sdk)
• Click on this checkbox to rebase all open PRs at once

Detected dependencies

devcontainer

.devcontainer/devcontainer.json

• ghcr.io/devcontainers/features/github-cli 1@sha256:464564228ccdd6028f01f8a62a3cfbaf76e9ba7953b29ac0e53ba2c262604312
• ghcr.io/devcontainers/features/docker-in-docker 2.9@sha256:9074d8eaf4585ab1498c81a8762078992725614fc7a9cfafe799aa22717a6bbf

dockerfile

modules/nf-core/bcl2fastq/Dockerfile

• debian bullseye-slim

modules/nf-core/bclconvert/Dockerfile

• docker/dockerfile 1
• debian bullseye-slim

modules/nf-core/cellranger/Dockerfile

• docker.io/continuumio/miniconda3 22.11.1@sha256:10b38c9a8a51692838ce4517e8c74515499b68d58c8a2000d8a9df7f0f08fc5e

modules/nf-core/cellranger/mkfastq/Dockerfile

• continuumio/miniconda3 4.8.2

modules/nf-core/cellrangerarc/Dockerfile

• continuumio/miniconda3 4.8.2

modules/nf-core/cellrangerarc/mkfastq/Dockerfile

• continuumio/miniconda3 4.8.2

modules/nf-core/cellrangeratac/Dockerfile

• continuumio/miniconda3 4.8.2

modules/nf-core/cellrangeratac/mkfastq/Dockerfile

• continuumio/miniconda3 4.8.2

modules/nf-core/coreograph/Dockerfile

• tensorflow/tensorflow 1.15.0-py3

modules/nf-core/ensemblvep/Dockerfile

• nfcore/base 1.14

modules/nf-core/quartonotebook/Dockerfile

• ubuntu 20.04
• condaforge/mambaforge 24.1.2-0@sha256:64c45c1a743737f61cf201f54cae974b5c853be94f9c1a84f5e82e0e854f0407

modules/nf-core/snpeff/Dockerfile

• nfcore/base 2.1

modules/nf-core/spaceranger/Dockerfile

• continuumio/miniconda3 4.9.2

modules/nf-core/wittyer/Dockerfile

• mcr.microsoft.com/dotnet/sdk 6.0@sha256:6df1177e48b55272316d08f19cb383483af82aca5cdc67a76c414bc200847624
• mcr.microsoft.com/dotnet/runtime 6.0@sha256:437cda84bdce26ce074d88b63abeec567c7226d73e8b911605077468e1d5c8d5

modules/nf-core/xeniumranger/Dockerfile

• ubuntu 20.04
• ubuntu 20.04

github-actions

.github/workflows/clean-up.yml

• actions/stale v9@28ca1036281a5e5922ead5184a1bbf96e5fc984e

.github/workflows/fix-linting.yml

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• peter-evans/create-or-update-comment v4@71345be0265236311c031f5c7866368bd1eff043
• actions/setup-node v4@39370e3970a6d050c480ffad4ff0ed4d3fdee5af
• peter-evans/create-or-update-comment v4@71345be0265236311c031f5c7866368bd1eff043

.github/workflows/test.yml

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-python v5@0b93645e9fea7318ecaed2b359559ac225c90a2b
• pre-commit/action v3.0.1@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd
• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-node v4@39370e3970a6d050c480ffad4ff0ed4d3fdee5af
• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-node v4@39370e3970a6d050c480ffad4ff0ed4d3fdee5af
• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• mirpedrol/paths-filter main
• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• adamrtalbot/detect-nf-test-changes v0.0.4@7c8be3ffd0d6538312b363c8c949dbbf5f26c3dd
• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-python v5@0b93645e9fea7318ecaed2b359559ac225c90a2b
• actions/cache v4@6849a6489940f00c2f30c0fb92c6274307ccb58a
• actions/setup-java v4@8df1039502a15bceb9433410b1a100fbe190c53b
• nf-core/setup-nextflow v2
• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-python v5@0b93645e9fea7318ecaed2b359559ac225c90a2b
• actions/setup-java v4@8df1039502a15bceb9433410b1a100fbe190c53b
• nf-core/setup-nextflow v2@561fcfc7146dcb12e3871909b635ab092a781f34
• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-python v5@0b93645e9fea7318ecaed2b359559ac225c90a2b
• actions/cache v4@6849a6489940f00c2f30c0fb92c6274307ccb58a
• actions/setup-java v4@8df1039502a15bceb9433410b1a100fbe190c53b
• nf-core/setup-nextflow v2
• eWaterCycle/setup-apptainer main
• conda-incubator/setup-miniconda v3@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d
• actions/github-script v7@60a0d83039c74a4aee543508d2ffcb1c3799cdea
• actions/upload-artifact v4@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882
• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/setup-java v4@8df1039502a15bceb9433410b1a100fbe190c53b
• nf-core/setup-nextflow v2
• nf-core/setup-nf-test v1
• eWaterCycle/setup-apptainer main
• actions/setup-python v5@0b93645e9fea7318ecaed2b359559ac225c90a2b
• actions/cache v4@6849a6489940f00c2f30c0fb92c6274307ccb58a
• conda-incubator/setup-miniconda v3@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d
• pcolby/tap-summary v1@0959cbe1d4422e62afc65778cdaea6716c41d936

.github/workflows/wave.yml

• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• tj-actions/changed-files v45@4edd678ac3f81e2dc578756871e4d00c19191daf
• actions/checkout v4@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/github-script v7@60a0d83039c74a4aee543508d2ffcb1c3799cdea

pre-commit

.pre-commit-config.yaml

• pre-commit/mirrors-prettier v3.1.0
• python-jsonschema/check-jsonschema 0.29.4
• astral-sh/ruff-pre-commit v0.7.3

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