Renovate Dashboard 🤖 #4211
Description
This issue lists Renovate updates and detected dependencies. Read the Dependency Dashboard docs to learn more.
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Repository Problems
These problems occurred while renovating this repository. View logs.
⚠️ WARN: Package lookup failures
Abandoned Dependencies
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.
These dependencies have not received updates for an extended period and may be unmaintained:
View abandoned dependencies (6)
| Datasource | Package | Last Updated |
|---|---|---|
| github-actions | adamrtalbot/detect-nf-test-changes | 2024-11-30 |
| github-actions | dorny/paths-filter | 2024-03-02 |
| 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.
- chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.15.5
- chore(deps): update pre-commit hook seqeralabs/nf-lint-pre-commit to v0.3.0
- 🔐 Create all awaiting schedule PRs at once 🔐
Warning
Renovate failed to look up the following dependencies: 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 davidfrantz/force, Failed to look up docker package python, Failed to look up docker package nfcore/base, Failed to look up docker package mambaorg/micromamba, Failed to look up docker package ubuntu, Failed to look up github-releases package nextflow/nextflow.
Files affected: modules/nf-core/bclconvert/Dockerfile, modules/nf-core/cellranger/Dockerfile.manual, modules/nf-core/cellranger/mkfastq/Dockerfile.manual, 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/force/cube/Dockerfile, modules/nf-core/force/tileextent/Dockerfile, modules/nf-core/opt/Dockerfile, modules/nf-core/snpeff/Dockerfile, modules/nf-core/spaceranger/Dockerfile, modules/nf-core/vizgenpostprocessing/Dockerfile, modules/nf-core/vuegen/Dockerfile, modules/nf-core/wittyer/Dockerfile, modules/nf-core/xeniumranger/Dockerfile, .github/workflows/lint.yml, .github/workflows/nf-test.yml, .github/workflows/update-gpu-snapshot.yml, .github/workflows/update-sentieon-snapshot.yml
Open
The following updates have all been created. To force a retry/rebase of any, click on a checkbox below.
- chore(deps): pin dependencies (
ghcr.io/qbic-pipelines/matlabruntime-base,quay.io/biocontainers/antismash) - chore(deps): update dotnet monorepo (
mcr.microsoft.com/dotnet/runtime,mcr.microsoft.com/dotnet/sdk) - chore(deps): update quay.io/biocontainers/antismash docker tag to v8.0.4
- chore(deps): update dotnet monorepo to v10 (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 (1)
.devcontainer/devcontainer.json
dockerfile (20)
modules/nf-core/antismash/Dockerfile (1)
quay.io/biocontainers/antismash 8.0.1--pyhdfd78af_0→ [Updates:8.0.4--pyhdfd78af_0,8.0.1--pyhdfd78af_0]modules/nf-core/bcl2fastq/Dockerfile (1)
debian bullseye-slimmodules/nf-core/bclconvert/Dockerfile (3)
docker/dockerfile 1debian bullseye-slimdebian bullseye-slimmodules/nf-core/cellranger/Dockerfile.manual (1)
continuumio/miniconda3 24.1.2-0modules/nf-core/cellranger/mkfastq/Dockerfile.manual (1)
continuumio/miniconda3 24.1.2-0modules/nf-core/cellrangerarc/Dockerfile (1)
continuumio/miniconda3 4.8.2modules/nf-core/cellrangerarc/mkfastq/Dockerfile (1)
continuumio/miniconda3 4.8.2modules/nf-core/cellrangeratac/Dockerfile (1)
continuumio/miniconda3 4.8.2modules/nf-core/cellrangeratac/mkfastq/Dockerfile (1)
continuumio/miniconda3 4.8.2modules/nf-core/coreograph/Dockerfile (1)
tensorflow/tensorflow 1.15.0-py3modules/nf-core/force/cube/Dockerfile (1)
davidfrantz/force 3.8.01modules/nf-core/force/tileextent/Dockerfile (1)
davidfrantz/force 3.8.01modules/nf-core/mat2json/Dockerfile (1)
ghcr.io/qbic-pipelines/matlabruntime-base 1.0.0→ [Updates:1.0.0]modules/nf-core/opt/Dockerfile (1)
python 3.11-slimmodules/nf-core/snpeff/Dockerfile (1)
nfcore/base 2.1modules/nf-core/spaceranger/Dockerfile (2)
docker/dockerfile 1mambaorg/micromamba 1.5.10-jammymodules/nf-core/vizgenpostprocessing/Dockerfile (1)
python 3.10-slim-bookwormmodules/nf-core/vuegen/Dockerfile (1)
python 3.12-slim-trixiemodules/nf-core/wittyer/Dockerfile (3)
docker/dockerfile 1-labsmcr.microsoft.com/dotnet/sdk 9.0@sha256:7d24e90a392e88eb56093e4eb325ff883ad609382a55d42f17fd557b997022ca→ [Updates:10.0,9.0]mcr.microsoft.com/dotnet/runtime 9.0@sha256:1e5eb0ed94ca96a34a914456db80e48bd1bb7bc3e3c8eda5e2c3d89c153c3081→ [Updates:10.0,9.0]modules/nf-core/xeniumranger/Dockerfile (2)
ubuntu 20.04ubuntu 20.04
github-actions (15)
.github/actions/get-shards/action.yml (2)
actions/setup-java v5@be666c2fcd27ec809703dec50e508c2fdc7f6654nf-core/setup-nf-test v1→ [Updates:v1].github/actions/nf-test-action/action.yml (6)
actions/setup-java v5@be666c2fcd27ec809703dec50e508c2fdc7f6654nf-core/setup-nextflow v2→ [Updates:v2]actions/setup-python v6@a309ff8b426b58ec0e2a45f0f869d46889d02405nf-core/setup-nf-test v1→ [Updates:v1]conda-incubator/setup-miniconda v3@fc2d68f6413eb2d87b895e92f8584b5b94a10167python 3.14.github/workflows/clean-up.yml (1)
actions/stale v10@b5d41d4e1d5dceea10e7104786b73624c18a190f.github/workflows/close-wishlist.yml (1)
actions/stale v10@b5d41d4e1d5dceea10e7104786b73624c18a190f.github/workflows/fix-linting.yml (4)
actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83ddpeter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9j178/prek-action v1@0bb87d7f00b0c99306c8bcb8b8beba1eb581c037peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9.github/workflows/label-wishlist.yml (1)
actions/github-script v8@ed597411d8f924073f98dfc5c65a23a2325f34cd.github/workflows/labeler.yml (1)
codelytv/pr-size-labeler v1@4ec67706cd878fbc1c8db0a5dcd28b6bb412e85a.github/workflows/lint.yml (17)
actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83ddnf-core/setup-nextflow v2→ [Updates:v2]j178/prek-action v1@0bb87d7f00b0c99306c8bcb8b8beba1eb581c037actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dddorny/paths-filter v3@de90cc6fb38fc0963ad72b210f1f284cd68cea36actions/github-script v8@ed597411d8f924073f98dfc5c65a23a2325f34cdactions/github-script v8@ed597411d8f924073f98dfc5c65a23a2325f34cdactions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83ddactions/setup-python v6@a309ff8b426b58ec0e2a45f0f869d46889d02405actions/cache v5@cdf6c1fa76f9f475f3d7449005a359c84ca0f306actions/setup-java v5@be666c2fcd27ec809703dec50e508c2fdc7f6654nf-core/setup-nextflow v2→ [Updates:v2]actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83ddactions/setup-python v6@a309ff8b426b58ec0e2a45f0f869d46889d02405nf-core/setup-nextflow v2→ [Updates:v2]python 3.14python 3.14.github/workflows/nf-test-gpu.yml (3)
actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83ddadamrtalbot/detect-nf-test-changes v0.0.6@de3c3c8e113031b4f15a3c1104b5f135e8346997actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd.github/workflows/nf-test.yml (3)
actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83ddadamrtalbot/detect-nf-test-changes v0.0.6@de3c3c8e113031b4f15a3c1104b5f135e8346997actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd.github/workflows/reminder.yml (1)
actions/stale v10@b5d41d4e1d5dceea10e7104786b73624c18a190f.github/workflows/skipped-nf-test-gpu.yml (2)
actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dddorny/paths-filter v3@de90cc6fb38fc0963ad72b210f1f284cd68cea36.github/workflows/skipped-nf-test.yml (2)
actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dddorny/paths-filter v3@de90cc6fb38fc0963ad72b210f1f284cd68cea36.github/workflows/update-gpu-snapshot.yml (8)
peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83ddpeter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9actions/setup-java v5@be666c2fcd27ec809703dec50e508c2fdc7f6654nf-core/setup-nextflow v2→ [Updates:v2]actions/setup-python v6@a309ff8b426b58ec0e2a45f0f869d46889d02405nf-core/setup-nf-test v1→ [Updates:v1]python 3.14.github/workflows/update-sentieon-snapshot.yml (8)
peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83ddpeter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9actions/setup-java v5@be666c2fcd27ec809703dec50e508c2fdc7f6654nf-core/setup-nextflow v2→ [Updates:v2]actions/setup-python v6@a309ff8b426b58ec0e2a45f0f869d46889d02405nf-core/setup-nf-test v1→ [Updates:v1]python 3.14
pre-commit (1)
.pre-commit-config.yaml (6)
pre-commit/mirrors-prettier v3.1.0pre-commit/pre-commit-hooks v6.0.0python-jsonschema/check-jsonschema 0.37.0astral-sh/ruff-pre-commit v0.15.4→ [Updates:v0.15.5]hadolint/hadolint v2.14.0seqeralabs/nf-lint-pre-commit v0.2.0→ [Updates:v0.3.0]
regex (6)
.github/workflows/lint.yml (1)
nextflow/nextflow 25.10.2.github/workflows/nf-test-gpu.yml (2)
askimed/nf-test 0.9.4nextflow-io/nextflow 25.10.4.github/workflows/nf-test.yml (2)
askimed/nf-test 0.9.4nextflow/nextflow 25.10.2.github/workflows/update-gpu-snapshot.yml (2)
askimed/nf-test 0.9.4nextflow/nextflow 25.10.2.github/workflows/update-sentieon-snapshot.yml (2)
askimed/nf-test 0.9.4nextflow/nextflow 25.10.2.pre-commit-config.yaml (1)
prettier 3.8.1
renovate-config-presets (1)
.github/renovate.json5
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