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[BATCH] Module updates that do not require pipeline updates
#8239 · famosab opened on Apr 8, 2025
2
[BATCH] Module updates requiring pipeline updates
#8238 · famosab opened on Apr 8, 2025
1
Renovate Dashboard 🤖
#4211 · renovate opened on Oct 24, 2023

Tests should create fixture files with collectFile instead of writing to launchDir or moduleDir
nf-core/modules#13423 · opened on Oct 20, 2026
2
Track modules that still ship a Dockerfile
nf-core/modules#13412 · opened on Oct 19, 2026
Update roary module to use Seqera containers
Task
nf-core/modules#13398 · opened on Oct 19, 2026
new module: tchem/detect and tchem/fetchlists
nf-core/modules#13385 · opened on Oct 18, 2026
Update taxonkit/lca, taxonkit/lineage, taxonkit/list, taxonkit/name2taxid to use Seqera Containers
nf-core/modules#13370 · opened on Oct 17, 2026
Update viennarna/rnacofold, viennarna/rnafold, and viennarna/rnalfold to use Seqera containers
Task
nf-core/modules#13351 · opened on Oct 16, 2026
Update blat to seqera containers
nf-core/modules#13346 · opened on Oct 16, 2026
New module: vardictrust
nf-core/modules#13343 · opened on Oct 16, 2026
Update blast to seqera containers
nf-core/modules#13340 · opened on Oct 16, 2026
Update bftools to seqera containers
nf-core/modules#13313 · opened on Oct 16, 2026
Seqera Container failing for gridss/somaticfilter
nf-core/modules#13272 · opened on Oct 16, 2026
1
Update quilt/quilt and quilt/quilt2 to use Seqera Containers
Task
nf-core/modules#13269 · opened on Oct 16, 2026
Update gridss/annotate, gridss/assemble, gridss/call, gridss/extractoverlappingfragments, gridss/generateponbedpe, gridss/gridss, gridss/preprocess, gridss/somaticfilter to use Seqera Containers
Task
nf-core/modules#13265 · opened on Oct 16, 2026
Update module bamutil to seqera container
nf-core/modules#13230 · opened on Oct 15, 2026
star/genomegenerate: --limitGenomeGenerateRAM leaves only 100 MB below task memory, so the container limit can kill STAR
nf-core/modules#13226 · opened on Oct 15, 2026
Update vt/normalize to use Seqera Containers
Task
nf-core/modules#13205 · opened on Oct 15, 2026
Update vt/decomposeblocksub to use Seqera Containers
Task
nf-core/modules#13204 · opened on Oct 15, 2026
Update vt/decompose to use Seqera Containers
Task
nf-core/modules#13203 · opened on Oct 15, 2026
Migrate remaining Biocontainers modules to Seqera Containers
Task
nf-core/modules#13143 · opened on Oct 13, 2026
Wrong URL for nf-core documentation
nf-core/modules#13113 · opened on Oct 9, 2026
update module: KRAKEN2/* 2.1.6 -> 2.17.2
nf-core/modules#13078 · opened on Oct 2, 2026
1
jellyfish/count crashes on paired-end input
nf-core/modules#13048 · opened on Sep 28, 2026
new module: instanexus/assemble
nf-core/modules#13044 · opened on Sep 28, 2026
new module: hmmibd-rs (no subtool needed)
Enhancement
nf-core/modules#13038 · opened on Sep 26, 2026
Permission issue with bcl2fastq creating InterOp
nf-core/modules#13034 · opened on Sep 25, 2026

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Issues

Tests should create fixture files with collectFile instead of writing to launchDir or moduleDir

Track modules that still ship a Dockerfile

Update `roary` module to use Seqera containers

new module: tchem/detect and tchem/fetchlists

Update `taxonkit/lca`, `taxonkit/lineage`, `taxonkit/list`, `taxonkit/name2taxid` to use Seqera Containers

Update `viennarna/rnacofold`, `viennarna/rnafold`, and `viennarna/rnalfold` to use Seqera containers

Update `blat` to seqera containers

New module: vardictrust

Update `blast` to seqera containers

Update `bftools` to seqera containers

Seqera Container failing for gridss/somaticfilter

Update `quilt/quilt` and `quilt/quilt2` to use Seqera Containers

Update `gridss/annotate`, `gridss/assemble`, `gridss/call`, `gridss/extractoverlappingfragments`, `gridss/generateponbedpe`, `gridss/gridss`, `gridss/preprocess`, `gridss/somaticfilter` to use Seqera Containers

Update module `bamutil` to seqera container

star/genomegenerate: --limitGenomeGenerateRAM leaves only 100 MB below task memory, so the container limit can kill STAR

Update `vt/normalize` to use Seqera Containers

Update `vt/decomposeblocksub` to use Seqera Containers

Update `vt/decompose` to use Seqera Containers

Migrate remaining Biocontainers modules to Seqera Containers

Wrong URL for nf-core documentation

update module: KRAKEN2/* 2.1.6 -> 2.17.2

jellyfish/count crashes on paired-end input

new module: instanexus/assemble

new module: hmmibd-rs (no subtool needed)

Permission issue with bcl2fastq creating InterOp