Track modules that still ship a Dockerfile

Aperta
  • Qualcosa non va?
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Valutazione

Difficoltà
4/5
Tempo stimato
3-5 giorni
Idoneità per principianti
35/100
Tipo di issue
Funzionalità
Chiarezza
Abbastanza chiara
Stato di attività
Attiva
Stack tecnologico
docker
Ambito
build-system, devops, infrastructure

Direzione di ricerca

Start by reading the Dockerfiles and module definitions under modules/nf-core, especially the entries listed in the status table, and check the related linting issue #7781. Work through the unchecked tasks: migrate eligible modules to Wave, record licensing terms for retained images, and resolve the force and wittyer decisions. Done means the table and task list record the outcomes and required licensing or lint follow-ups; the Wave builds still need testing.

Scritto dal modello di indicizzazione a partire dal testo della issue.

Descrizione

Summary

22 Dockerfiles remain in modules/nf-core. This issue tracks, for each one, whether it can be removed and the container rebuilt with Wave (via nf-core modules containers), or whether it must stay. Where it stays, the reason (usually licensing) should be recorded here so it survives core team rotations.

Some Dockerfiles sit at tool-folder level and are shared by every subcommand module in that folder (e.g. antismash/Dockerfile, cellranger/Dockerfile.manual, vizgenpostprocessing/Dockerfile). Removing one affects all of those modules.

Related:

  • #7781: linting fails for modules with a Dockerfile. The modules marked Keep below are the ones that would need a lint exemption.
  • #4211: Renovate dashboard

Thanks to @jfy133, @maxulysse, @pontus, @sppearce for the input.

Status

Legend: 🟢 remove and migrate to Wave · 🟡 needs work or a decision · 🔴 keep (Dockerfile required)

Module Verdict Finding Licence / permission record
snpeff 🟢 Remove Owner agreed to removal -
vizgenpostprocessing (compiletilesegmentation, preparesegmentation, runsegmentationontile) 🟢 Remove Dockerfile only does pip install vpt vpt-plugin-cellpose2. Both are on bioconda (vpt 1.3.0). Need to check that conda covers libvips, Java and libGL Apache-2.0
coreograph 🟢 Remove The module uses docker.io/labsyspharm/unetcoreograph:2.2.9; the local Dockerfile is an unused upstream copy. bioconda has unetcoreograph 2.4.6. Needs a version bump and testing; the bioconda recipe does not list TensorFlow MIT
force/cube, force/tileextent 🟡 Delete Dockerfile Dockerfile is only FROM davidfrantz/force:3.8.01 (mirrored to quay.io). Not on conda, so Wave needs a bioconda recipe first (C code with GDAL). Decide: keep the quay mirror or point to the upstream image GPL-3.0
antismash (antismash, antismashdownloaddatabases) 🔴 Keep Build bakes antiSMASH's data cache into the image, then deletes the database. Containers are read-only, so the cache cannot be written at runtime (see antismash/README.md). Wave cannot run this build step. The -lite modules already use biocontainers AGPL-3.0, open source
wittyer 🔴 Keep, check licence Built from source with .NET; not on conda. Upstream repo is archived (2023). Should we deprecate the module? GitHub detects no licence; LICENSE.md covers only third-party components. Unclear
mat2json 🔴 Keep Needs MATLAB Runtime (proprietary) via a ghcr.io/qbic-pipelines/matlabruntime-* base image; not on conda Tool MIT; MATLAB Runtime under MathWorks terms. Record redistribution terms
numorph/intensity, numorph/resample 🔴 Keep Same MATLAB Runtime setup as mat2json Same as mat2json
numorph/3dunet 🔴 Keep (probably) numorph-3dunet (PyPI) requires Python 3.6, uses NVIDIA's TensorFlow 1 GPU image (nvcr.io) as its base, and installs keras-contrib from git. conda-forge's newest 1.x TensorFlow is 1.14. A Wave build would be fragile and lose the NVIDIA GPU optimisations Tool MIT; NVIDIA container licence. Check redistribution
cellranger, cellranger/mkfastq 🔴 Keep 10x Genomics commercial software Link 10x agreement
cellrangerarc, cellrangerarc/mkfastq 🔴 Keep 10x Genomics commercial software Link 10x agreement
cellrangeratac, cellrangeratac/mkfastq 🔴 Keep 10x Genomics commercial software Link 10x agreement
spaceranger 🔴 Keep 10x Genomics commercial software Link 10x agreement
xeniumranger 🔴 Keep 10x Genomics commercial software Link 10x agreement
universc 🔴 Keep Depends on 10x software Link 10x agreement
bcl2fastq 🔴 Keep Illumina commercial software Link Illumina terms
bclconvert 🔴 Keep Illumina commercial software Link Illumina terms

Findings for the 🟢/🟡 rows come from package listings and licence files only. None of the Wave builds has been tested yet.

Tasks

🟢 Remove and migrate to Wave
  • snpeff
  • vizgenpostprocessing
  • coreograph (incl. bump to 2.4.6)
🟡 Needs work or a decision
  • force/cube, force/tileextent: delete Dockerfile; decide between the quay mirror and the upstream image
  • wittyer: clarify the licence; decide whether to deprecate
🔴 Keep: record why
  • 10x modules: link the agreement that lets nf-core distribute these images
  • Illumina modules (bcl2fastq, bclconvert): link redistribution terms
  • MATLAB Runtime modules (mat2json, numorph/intensity, numorph/resample): record the MathWorks redistribution terms
  • numorph/3dunet: confirm the NVIDIA base image may be redistributed
  • antismash: no action unless upstream changes how it caches data
Follow-up
  • Agree on a lint exemption for the 🔴 modules, so #7781 can be closed

If you own one of these modules or know the licensing background, please comment so the table can be updated. Removal PRs should reference this issue ("Part of #NNNN").

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