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[renovate]

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

These dependencies have not received updates for an extended period and may be unmaintained:

View abandoned dependencies (7)

Datasource	Name	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

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.

Awaiting Schedule

The following updates are awaiting their schedule. To get an update now, click on a checkbox below.

• chore(deps): update dependency prettier to v3.7.4
• chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.14.11
• chore(deps): update dependency seqeralabs/wave-cli to v1.8.1
• chore(deps): update pre-commit hook python-jsonschema/check-jsonschema to v0.36.0
• chore(deps): update dependency nextflow-io/nextflow to v25
• chore(deps): update dotnet monorepo to v10 (major) (mcr.microsoft.com/dotnet/runtime, mcr.microsoft.com/dotnet/sdk)
• 🔐 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.

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/xeniumranger/Dockerfile

---

Open

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

• chore(deps): update dotnet monorepo (mcr.microsoft.com/dotnet/runtime, mcr.microsoft.com/dotnet/sdk)

PR Closed (Blocked)

The following updates are blocked by an existing closed PR. To recreate the PR, click on a checkbox below.

• chore(deps): pin quay.io/biocontainers/antismash docker tag to 9977bae
• chore(deps): update quay.io/biocontainers/antismash docker tag to v8.0.4

Detected Dependencies

devcontainer (1)

.devcontainer/devcontainer.json

dockerfile (19)

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-slim

modules/nf-core/bclconvert/Dockerfile (2)

• docker/dockerfile 1
• debian bullseye-slim

modules/nf-core/cellranger/Dockerfile.manual (1)

• continuumio/miniconda3 24.1.2-0

modules/nf-core/cellranger/mkfastq/Dockerfile.manual (1)

• continuumio/miniconda3 24.1.2-0

modules/nf-core/cellrangerarc/Dockerfile (1)

• continuumio/miniconda3 4.8.2

modules/nf-core/cellrangerarc/mkfastq/Dockerfile (1)

• continuumio/miniconda3 4.8.2

modules/nf-core/cellrangeratac/Dockerfile (1)

• continuumio/miniconda3 4.8.2

modules/nf-core/cellrangeratac/mkfastq/Dockerfile (1)

• continuumio/miniconda3 4.8.2

modules/nf-core/coreograph/Dockerfile (1)

• tensorflow/tensorflow 1.15.0-py3

modules/nf-core/force/cube/Dockerfile (1)

• davidfrantz/force 3.8.01

modules/nf-core/force/tileextent/Dockerfile (1)

• davidfrantz/force 3.8.01

modules/nf-core/opt/Dockerfile (1)

• python 3.11-slim

modules/nf-core/snpeff/Dockerfile (1)

• nfcore/base 2.1

modules/nf-core/spaceranger/Dockerfile (2)

• docker/dockerfile 1
• mambaorg/micromamba 1.5.10-jammy

modules/nf-core/vizgenpostprocessing/Dockerfile (1)

• python 3.10-slim-bookworm

modules/nf-core/vuegen/Dockerfile (1)

• python 3.12-slim-trixie

modules/nf-core/wittyer/Dockerfile (2)

• mcr.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 20.04
• ubuntu 20.04

github-actions (16)

.github/actions/get-shards/action.yml (1)

• nf-core/setup-nf-test v1 → [Updates: v1]

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

• actions/setup-java v5@f2beeb24e141e01a676f977032f5a29d81c9e27e
• nf-core/setup-nextflow v2 → [Updates: v2]
• actions/setup-python v6@83679a892e2d95755f2dac6acb0bfd1e9ac5d548
• nf-core/setup-nf-test v1 → [Updates: v1]
• conda-incubator/setup-miniconda v3@835234971496cad1653abb28a638a281cf32541f
• python 3.14

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

• actions/stale v10@997185467fa4f803885201cee163a9f38240193d

.github/workflows/close-wishlist.yml (1)

• actions/stale v10@997185467fa4f803885201cee163a9f38240193d

.github/workflows/fix-linting.yml (4)

• actions/checkout v6@8e8c483db84b4bee98b60c0593521ed34d9990e8
• peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
• j178/prek-action v1@91fd7d7cf70ae1dee9f4f44e7dfa5d1073fe6623
• peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9

.github/workflows/label-wishlist.yml (1)

• actions/github-script v8@ed597411d8f924073f98dfc5c65a23a2325f34cd

.github/workflows/lint.yml (16)

• actions/checkout v6@8e8c483db84b4bee98b60c0593521ed34d9990e8
• j178/prek-action v1@91fd7d7cf70ae1dee9f4f44e7dfa5d1073fe6623
• actions/checkout v6@8e8c483db84b4bee98b60c0593521ed34d9990e8
• dorny/paths-filter v3@de90cc6fb38fc0963ad72b210f1f284cd68cea36
• actions/github-script v8@ed597411d8f924073f98dfc5c65a23a2325f34cd
• actions/github-script v8@ed597411d8f924073f98dfc5c65a23a2325f34cd
• actions/checkout v6@8e8c483db84b4bee98b60c0593521ed34d9990e8
• actions/setup-python v6@83679a892e2d95755f2dac6acb0bfd1e9ac5d548
• actions/cache v5@9255dc7a253b0ccc959486e2bca901246202afeb
• actions/setup-java v5@f2beeb24e141e01a676f977032f5a29d81c9e27e
• nf-core/setup-nextflow v2 → [Updates: v2]
• actions/checkout v6@8e8c483db84b4bee98b60c0593521ed34d9990e8
• actions/setup-python v6@83679a892e2d95755f2dac6acb0bfd1e9ac5d548
• nf-core/setup-nextflow v2 → [Updates: v2]
• python 3.14
• python 3.14

.github/workflows/nf-test-gpu.yml (3)

• actions/checkout v6@8e8c483db84b4bee98b60c0593521ed34d9990e8
• adamrtalbot/detect-nf-test-changes v0.0.6@de3c3c8e113031b4f15a3c1104b5f135e8346997
• actions/checkout v6@8e8c483db84b4bee98b60c0593521ed34d9990e8

.github/workflows/nf-test.yml (3)

• actions/checkout v6@8e8c483db84b4bee98b60c0593521ed34d9990e8
• adamrtalbot/detect-nf-test-changes v0.0.6@de3c3c8e113031b4f15a3c1104b5f135e8346997
• actions/checkout v6@8e8c483db84b4bee98b60c0593521ed34d9990e8

.github/workflows/pytest-workflow.yml (12)

• actions/checkout v6@8e8c483db84b4bee98b60c0593521ed34d9990e8
• dorny/paths-filter v3@de90cc6fb38fc0963ad72b210f1f284cd68cea36
• actions/checkout v6@8e8c483db84b4bee98b60c0593521ed34d9990e8
• actions/setup-python v6@83679a892e2d95755f2dac6acb0bfd1e9ac5d548
• actions/cache v5@9255dc7a253b0ccc959486e2bca901246202afeb
• actions/setup-java v5@f2beeb24e141e01a676f977032f5a29d81c9e27e
• nf-core/setup-nextflow v2 → [Updates: v2]
• eWaterCycle/setup-apptainer main
• conda-incubator/setup-miniconda v3@835234971496cad1653abb28a638a281cf32541f
• actions/github-script v8@ed597411d8f924073f98dfc5c65a23a2325f34cd
• actions/upload-artifact v6@b7c566a772e6b6bfb58ed0dc250532a479d7789f
• python 3.14

.github/workflows/reminder.yml (1)

• actions/stale v10@997185467fa4f803885201cee163a9f38240193d

.github/workflows/skipped-nf-test-gpu.yml (2)

• actions/checkout v6@8e8c483db84b4bee98b60c0593521ed34d9990e8
• dorny/paths-filter v3@de90cc6fb38fc0963ad72b210f1f284cd68cea36

.github/workflows/skipped-nf-test.yml (2)

• actions/checkout v6@8e8c483db84b4bee98b60c0593521ed34d9990e8
• dorny/paths-filter v3@de90cc6fb38fc0963ad72b210f1f284cd68cea36

.github/workflows/update-gpu-snapshot.yml (8)

• peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
• actions/checkout v6@8e8c483db84b4bee98b60c0593521ed34d9990e8
• peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
• actions/setup-java v5@f2beeb24e141e01a676f977032f5a29d81c9e27e
• nf-core/setup-nextflow v2 → [Updates: v2]
• actions/setup-python v6@83679a892e2d95755f2dac6acb0bfd1e9ac5d548
• nf-core/setup-nf-test v1 → [Updates: v1]
• python 3.14

.github/workflows/update-sentieon-snapshot.yml (8)

• peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
• actions/checkout v6@8e8c483db84b4bee98b60c0593521ed34d9990e8
• peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
• actions/setup-java v5@f2beeb24e141e01a676f977032f5a29d81c9e27e
• nf-core/setup-nextflow v2 → [Updates: v2]
• actions/setup-python v6@83679a892e2d95755f2dac6acb0bfd1e9ac5d548
• nf-core/setup-nf-test v1 → [Updates: v1]
• python 3.14

.github/workflows/wave.yml (6)

• actions/checkout v6@8e8c483db84b4bee98b60c0593521ed34d9990e8
• tj-actions/changed-files v47@24d32ffd492484c1d75e0c0b894501ddb9d30d62
• tj-actions/changed-files v47@24d32ffd492484c1d75e0c0b894501ddb9d30d62
• actions/checkout v6@8e8c483db84b4bee98b60c0593521ed34d9990e8
• actions/checkout v6@8e8c483db84b4bee98b60c0593521ed34d9990e8
• actions/github-script v8@ed597411d8f924073f98dfc5c65a23a2325f34cd

pre-commit (1)

.pre-commit-config.yaml (5)

• pre-commit/mirrors-prettier v3.1.0
• pre-commit/pre-commit-hooks v6.0.0
• python-jsonschema/check-jsonschema 0.35.0 → [Updates: 0.36.0]
• astral-sh/ruff-pre-commit v0.14.7 → [Updates: v0.14.11]
• hadolint/hadolint v2.14.0

regex (8)

.github/workflows/lint.yml

.github/workflows/nf-test-gpu.yml (1)

• askimed/nf-test 0.9.3

.github/workflows/nf-test.yml (1)

• askimed/nf-test 0.9.3

.github/workflows/pytest-workflow.yml (1)

• nextflow-io/nextflow 24.10.9 → [Updates: 25.10.2]

.github/workflows/update-gpu-snapshot.yml (1)

• askimed/nf-test 0.9.3

.github/workflows/update-sentieon-snapshot.yml (1)

• askimed/nf-test 0.9.3

.github/workflows/wave.yml (2)

• seqeralabs/wave-cli 1.7.0 → [Updates: 1.8.1]
• askimed/nf-test 0.9.3

.pre-commit-config.yaml (1)

• prettier 3.7.3 → [Updates: 3.7.4]

renovate-config-presets (1)

.github/renovate.json5

---

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