nf-core / nf-core/modules

Renovate Dashboard 🤖

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Nextflow
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Avg merge
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Merged PRs (30d)
153

Description

This issue lists Renovate updates and detected dependencies. Read the Dependency Dashboard docs to learn more.
View this repository on the Mend.io Web Portal.

Repository Problems

These problems occurred while renovating this repository. View logs.

  • ⚠️ WARN: Package lookup failures

Abandoned Dependencies

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

[!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.

View abandoned dependencies (2)
Datasource Package Last Updated
pre-commit pre-commit/mirrors-prettier 2023-12-21
pre-commit pre-commit/pre-commit-hooks 2025-08-09

Awaiting Schedule

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

  • Update nvcr.io/nvidia/tensorflow Docker tag to v20.12
  • Update dependency java-jdk to v25
  • Update dotnet monorepo to v11 (mcr.microsoft.com/dotnet/runtime, mcr.microsoft.com/dotnet/sdk)
  • Update nvcr.io/nvidia/tensorflow Docker tag to v23
  • 🔐 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 nfcore/base: no-result, Failed to look up docker package mambaorg/micromamba: no-result, Failed to look up docker package python: 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/snpeff/Dockerfile, modules/nf-core/spaceranger/Dockerfile, modules/nf-core/vizgenpostprocessing/Dockerfile, modules/nf-core/wittyer/Dockerfile, modules/nf-core/xeniumranger/Dockerfile, .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.

PR Closed (Blocked)

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

Detected Dependencies

devcontainer (1)
.devcontainer/devcontainer.json
dockerfile (21)
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/3dunet/Dockerfile (1)
  • nvcr.io/nvidia/tensorflow 20.10-tf1-py3@sha256:9206ed88af83ca5dd4ba6bd95cf6aff6f8432ce98699aa43c216222747dc4500 → [Updates: 20.12-tf1-py3, 23.03-tf1-py3]
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/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/wittyer/Dockerfile (3)
  • docker/dockerfile 1-labs
  • mcr.microsoft.com/dotnet/sdk 9.0@sha256:7d24e90a392e88eb56093e4eb325ff883ad609382a55d42f17fd557b997022ca → [Updates: 11.0, 9.0]
  • mcr.microsoft.com/dotnet/runtime 9.0@sha256:1e5eb0ed94ca96a34a914456db80e48bd1bb7bc3e3c8eda5e2c3d89c153c3081 → [Updates: 11.0, 9.0]
modules/nf-core/xeniumranger/Dockerfile (2)
  • ubuntu 20.04
  • ubuntu 20.04
github-actions (16)
.github/actions/detect-nf-test-changes/action.yml (3)
  • actions/setup-java v6@de7274f081f381c8f8158605e0321c36c376e2e6
  • nf-core/setup-nf-test v2@4069fbbaabe94c08faba4ad261bfa88225ba133f
  • java-jdk 17 → [Updates: 25]
.github/actions/get-shards/action.yml (3)
  • actions/setup-java v6@de7274f081f381c8f8158605e0321c36c376e2e6
  • nf-core/setup-nf-test v2@4069fbbaabe94c08faba4ad261bfa88225ba133f
  • java-jdk 17 → [Updates: 25]
.github/actions/nf-test-action/action.yml (7)
  • actions/setup-java v6@de7274f081f381c8f8158605e0321c36c376e2e6
  • nf-core/setup-nextflow v3@893c28b667aedeba26e37f296d260ccc5bc4d914
  • actions/setup-python v7@5fda3b95a4ea91299a34e894583c3862153e4b97
  • nf-core/setup-nf-test v2@4069fbbaabe94c08faba4ad261bfa88225ba133f
  • conda-incubator/setup-miniconda v4@8ee1f361103df19b6f8c8655fd3967a8ecb162d5
  • java-jdk 17 → [Updates: 25]
  • python 3.14
.github/workflows/clean-up.yml (1)
  • actions/stale v11@4391f3da665fdf50b6810c1a66712fb9ba21aa93
.github/workflows/close-wishlist.yml (1)
  • actions/stale v11@4391f3da665fdf50b6810c1a66712fb9ba21aa93
.github/workflows/fix-linting.yml (11)
  • peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • nf-core/setup-nextflow v3@893c28b667aedeba26e37f296d260ccc5bc4d914
  • j178/prek-action v3.0.0@4e14d07f9231acabce116ccfca13b13dd9755ece
  • actions/upload-artifact v7@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/download-artifact v8.0.1@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c
  • 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 (18)
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • nf-core/setup-nextflow v3@893c28b667aedeba26e37f296d260ccc5bc4d914
  • j178/prek-action v3.0.0@4e14d07f9231acabce116ccfca13b13dd9755ece
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • dorny/paths-filter v4@ceb8a2b8f2d89434be7ff52d3de7ec3738c5cc9d
  • actions/github-script v9@3a2844b7e9c422d3c10d287c895573f7108da1b3
  • actions/github-script v9@3a2844b7e9c422d3c10d287c895573f7108da1b3
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/setup-python v7@5fda3b95a4ea91299a34e894583c3862153e4b97
  • actions/cache v6.1.0@55cc8345863c7cc4c66a329aec7e433d2d1c52a9
  • actions/setup-java v6@de7274f081f381c8f8158605e0321c36c376e2e6
  • nf-core/setup-nextflow v3@893c28b667aedeba26e37f296d260ccc5bc4d914
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/setup-python v7@5fda3b95a4ea91299a34e894583c3862153e4b97
  • nf-core/setup-nextflow v3@893c28b667aedeba26e37f296d260ccc5bc4d914
  • python 3.14
  • java-jdk 17 → [Updates: 25]
  • python 3.14
.github/workflows/nf-test-gpu.yml (3)
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
.github/workflows/nf-test.yml (2)
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
.github/workflows/reminder.yml (1)
  • actions/stale v11@4391f3da665fdf50b6810c1a66712fb9ba21aa93
.github/workflows/skipped-nf-test-gpu.yml (2)
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • dorny/paths-filter v4@ceb8a2b8f2d89434be7ff52d3de7ec3738c5cc9d
.github/workflows/skipped-nf-test.yml (2)
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • dorny/paths-filter v4@ceb8a2b8f2d89434be7ff52d3de7ec3738c5cc9d
.github/workflows/update-gpu-snapshot.yml (12)
  • peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
  • peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/setup-java v6@de7274f081f381c8f8158605e0321c36c376e2e6
  • nf-core/setup-nextflow v3@893c28b667aedeba26e37f296d260ccc5bc4d914
  • actions/setup-python v7@5fda3b95a4ea91299a34e894583c3862153e4b97
  • nf-core/setup-nf-test v2@4069fbbaabe94c08faba4ad261bfa88225ba133f
  • actions/upload-artifact v7@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/download-artifact v8.0.1@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c
  • java-jdk 17 → [Updates: 25]
  • python 3.14
.github/workflows/update-sentieon-snapshot.yml (12)
  • peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
  • peter-evans/create-or-update-comment v5@e8674b075228eee787fea43ef493e45ece1004c9
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/setup-java v6@de7274f081f381c8f8158605e0321c36c376e2e6
  • nf-core/setup-nextflow v3@893c28b667aedeba26e37f296d260ccc5bc4d914
  • actions/setup-python v7@5fda3b95a4ea91299a34e894583c3862153e4b97
  • nf-core/setup-nf-test v2@4069fbbaabe94c08faba4ad261bfa88225ba133f
  • actions/upload-artifact v7@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
  • actions/checkout v7@3d3c42e5aac5ba805825da76410c181273ba90b1
  • actions/download-artifact v8.0.1@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c
  • java-jdk 17 → [Updates: 25]
  • 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 0.37.4 → [Updates: 0.38.0]
  • astral-sh/ruff-pre-commit v0.16.1 → [Updates: v0.16.8]
  • hadolint/hadolint v2.15.1
  • seqeralabs/nf-lint-pre-commit v0.3.0
regex (6)
.github/workflows/lint.yml
.github/workflows/nf-test-gpu.yml (2)
  • askimed/nf-test 0.9.5
  • nextflow-io/nextflow 25.10.7
.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 3.9.3 → [Updates: 3.9.6]
renovate-config (1)
.github/renovate.json5
  • Check this box to trigger a request for Renovate to run again on this repository

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the Renovate Dependency Dashboard documentation and the repository problems section, then inspect the listed Dockerfiles, GitHub Actions files, and existing pull requests. The issue aggregates dependency updates and package lookup failures rather than defining one change, so done is not specified; several updates are already covered by open PRs.

Written by the indexing model from the issue text.

Assessment

Tech stack
docker, github-actions, java, python
Domain
ci-cd, devops, tooling
Issue type
Refactor
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
15/100

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