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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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Abandoned Dependencies

The following dependencies have not received updates for an extended period and may be unmaintained.

View abandoned dependencies (4)

[!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.

Datasource	Package	Last Updated
github-actions	adamrtalbot/detect-nf-test-changes	2024-11-30
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.

• Update dotnet monorepo (mcr.microsoft.com/dotnet/runtime, mcr.microsoft.com/dotnet/sdk)
• Update dependency nextflow-io/nextflow to v25.10.5
• 🔐 Create all awaiting schedule PRs at once 🔐

---

Warning

Renovate failed to look up the following dependencies: Failed to look up docker package docker/dockerfile: no-result, Failed to look up docker package continuumio/miniconda3: no-result, Failed to look up docker package tensorflow/tensorflow: no-result, Failed to look up docker package davidfrantz/force: no-result, Failed to look up docker package python: no-result, Failed to look up docker package nfcore/base: no-result, Failed to look up docker package mambaorg/micromamba: no-result, Failed to look up docker package ubuntu: no-result, Failed to look up github-releases package nextflow/nextflow: no-result.

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/sushie/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.

• Update dotnet monorepo to v10 (major) (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.

• Update quay.io/biocontainers/antismash Docker tag to v8.0.4

Detected Dependencies

devcontainer (1)

.devcontainer/devcontainer.json

dockerfile (23)

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

• quay.io/biocontainers/antismash 8.0.1--pyhdfd78af_0@sha256:9977bae26a2635c33c20493d001ad6c8e01372ab7f7c2a11bb4b3612b8f8061a → [Updates: 8.0.4--pyhdfd78af_0]

modules/nf-core/bcl2fastq/Dockerfile (1)

• debian bullseye-slim

modules/nf-core/bclconvert/Dockerfile (3)

• docker/dockerfile 1
• debian bullseye-slim
• 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/mat2json/Dockerfile (1)

• ghcr.io/qbic-pipelines/matlabruntime-base 1.0.0@sha256:b1bacc5939d75034a1e9d01f3a294668f5f5b726977d15a7a4beca3e60b7ad0b

modules/nf-core/numorph/intensity/Dockerfile (1)

• ghcr.io/qbic-pipelines/matlabruntime-numorphtools 1.0.0@sha256:e05a941552a1f9c741530d68a0d3877363c8e05bb385190f0acade97db73656b

modules/nf-core/numorph/resample/Dockerfile (1)

• ghcr.io/qbic-pipelines/matlabruntime-numorphtools 1.0.0@sha256:e05a941552a1f9c741530d68a0d3877363c8e05bb385190f0acade97db73656b

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/sushie/Dockerfile (1)

• python 3.10-slim

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 (3)

• docker/dockerfile 1-labs
• 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 (15)

.github/actions/get-shards/action.yml (2)

• actions/setup-java v5@be666c2fcd27ec809703dec50e508c2fdc7f6654
• nf-core/setup-nf-test v2@4069fbbaabe94c08faba4ad261bfa88225ba133f

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

• actions/setup-java v5@be666c2fcd27ec809703dec50e508c2fdc7f6654
• nf-core/setup-nextflow v3@b4ec1bc7c16a94435159de94a05253542fddf6ef
• actions/setup-python v6@a309ff8b426b58ec0e2a45f0f869d46889d02405
• nf-core/setup-nf-test v2@4069fbbaabe94c08faba4ad261bfa88225ba133f
• conda-incubator/setup-miniconda v4@8ee1f361103df19b6f8c8655fd3967a8ecb162d5
• python 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 (7)

• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
• j178/prek-action v2.0.3@6ad80277337ad479fe43bd70701c3f7f8aa74db3
• peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
• peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
• peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
• peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9

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

• actions/github-script v9@3a2844b7e9c422d3c10d287c895573f7108da1b3

.github/workflows/labeler.yml (1)

• codelytv/pr-size-labeler v1@095a41fca88b8764fd9e008ad269bcdb82bb38b9

.github/workflows/lint.yml (17)

• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• nf-core/setup-nextflow v3@b4ec1bc7c16a94435159de94a05253542fddf6ef
• j178/prek-action v2.0.3@6ad80277337ad479fe43bd70701c3f7f8aa74db3
• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• dorny/paths-filter v4@fbd0ab8f3e69293af611ebaee6363fc25e6d187d
• actions/github-script v9@3a2844b7e9c422d3c10d287c895573f7108da1b3
• actions/github-script v9@3a2844b7e9c422d3c10d287c895573f7108da1b3
• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• actions/setup-python v6@a309ff8b426b58ec0e2a45f0f869d46889d02405
• actions/cache v5.0.5@27d5ce7f107fe9357f9df03efb73ab90386fccae
• actions/setup-java v5@be666c2fcd27ec809703dec50e508c2fdc7f6654
• nf-core/setup-nextflow v3@b4ec1bc7c16a94435159de94a05253542fddf6ef
• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• actions/setup-python v6@a309ff8b426b58ec0e2a45f0f869d46889d02405
• nf-core/setup-nextflow v3@b4ec1bc7c16a94435159de94a05253542fddf6ef
• python 3.14
• python 3.14

.github/workflows/nf-test-gpu.yml (5)

• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• adamrtalbot/detect-nf-test-changes v0.0.6@de3c3c8e113031b4f15a3c1104b5f135e8346997
• adamrtalbot/detect-nf-test-changes v0.0.6@de3c3c8e113031b4f15a3c1104b5f135e8346997
• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd

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

• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• adamrtalbot/detect-nf-test-changes v0.0.6@de3c3c8e113031b4f15a3c1104b5f135e8346997
• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd

.github/workflows/reminder.yml (1)

• actions/stale v10@b5d41d4e1d5dceea10e7104786b73624c18a190f

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

• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• dorny/paths-filter v4@fbd0ab8f3e69293af611ebaee6363fc25e6d187d

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

• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• dorny/paths-filter v4@fbd0ab8f3e69293af611ebaee6363fc25e6d187d

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

• peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
• actions/setup-java v5@be666c2fcd27ec809703dec50e508c2fdc7f6654
• nf-core/setup-nextflow v3@b4ec1bc7c16a94435159de94a05253542fddf6ef
• actions/setup-python v6@a309ff8b426b58ec0e2a45f0f869d46889d02405
• nf-core/setup-nf-test v2@4069fbbaabe94c08faba4ad261bfa88225ba133f
• python 3.14

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

• peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
• actions/checkout v6@de0fac2e4500dabe0009e67214ff5f5447ce83dd
• peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
• actions/setup-java v5@be666c2fcd27ec809703dec50e508c2fdc7f6654
• nf-core/setup-nextflow v3@b4ec1bc7c16a94435159de94a05253542fddf6ef
• actions/setup-python v6@a309ff8b426b58ec0e2a45f0f869d46889d02405
• nf-core/setup-nf-test v2@4069fbbaabe94c08faba4ad261bfa88225ba133f
• python 3.14

pre-commit (1)

.pre-commit-config.yaml (6)

• pre-commit/mirrors-prettier v3.1.0
• pre-commit/pre-commit-hooks v6.0.0
• python-jsonschema/check-jsonschema 0.37.2
• astral-sh/ruff-pre-commit v0.15.12
• hadolint/hadolint v2.14.0
• seqeralabs/nf-lint-pre-commit 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 0.9.5
• nextflow-io/nextflow 25.10.4 → [Updates: 25.10.5]

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

• askimed/nf-test 0.9.5
• nextflow/nextflow 25.10.2

.github/workflows/update-gpu-snapshot.yml (2)

• askimed/nf-test 0.9.5
• nextflow/nextflow 25.10.2

.github/workflows/update-sentieon-snapshot.yml (2)

• askimed/nf-test 0.9.5
• nextflow/nextflow 25.10.2

.pre-commit-config.yaml (1)

• prettier 3.8.3

renovate-config (1)

.github/renovate.json5

---

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