A community effort to collect a curated set of analysis pipelines built using Nextflow.
nf-core
Pipeline release! nf-core/pixelator v4.1.2 - nf-core/pixelator 4.1.2!
Please see the changelog: https://github.com/nf-core/pixelator/releases/tag/4.1.2
Pipeline release! nf-core/drugresponseeval v1.2.1 - Drugresponseeval 1.2.1 - Sleepy Snorlax!
Please see the changelog: https://github.com/nf-core/drugresponseeval/releases/tag/1.2.1
Pipeline release! nf-core/airrflow v5.1.0 - 5.1.0 - Ventus!
Please see the changelog: https://github.com/nf-core/airrflow/releases/tag/5.1.0
Pipeline release! nf-core/rnafusion v4.1.3 - 4.1.3!
Please see the changelog: https://github.com/nf-core/rnafusion/releases/tag/4.1.3
Pipeline release! nf-core/pairgenomealign v2.3.0 - nf-core/pairgenomealign v2.3.0 – Umi budou!
Please see the changelog: https://github.com/nf-core/pairgenomealign/releases/tag/2.3.0
Pipeline release! nf-core/proteinfamilies v2.4.0 - Titanium Falcon!
Please see the changelog: https://github.com/nf-core/proteinfamilies/releases/tag/2.4.0
Pipeline release! nf-core/viralmetagenome v1.1.2 - v1.1.2 - Blush Bunting!
Please see the changelog: https://github.com/nf-core/viralmetagenome/releases/tag/1.1.2
Pipeline release! nf-core/createpanelrefs v1.0.0 - nf-core/createpanelrefs 1.0.0 - Hell's Gate!
Please see the changelog: https://github.com/nf-core/createpanelrefs/releases/tag/1.0.0
Pipeline release! nf-core/rnavar v1.3.0 - nf-core/rnavar 1.3.0 - Silent Nostromo!
Please see the changelog: https://github.com/nf-core/rnavar/releases/tag/1.3.0
Pipeline release! nf-core/lsmquant v1.0.1 - Excited Squid Patch!
Please see the changelog: https://github.com/nf-core/lsmquant/releases/tag/1.0.1
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nf-core
v1.1.2 - 2026-06-03
Added
Add param --cluster_with_reference_pool to optionally include the reference pool in the clustering step (#278) (by @nrminor, @Joon-Klaps)
Template update to nf-core/tools...
[4.1.2] - 2026-06-04
Enhancements & fixes
Update pixelator container to 0.28.0. This fixes a major performance regression in the graph step, which caused very high memory usage. By @johandahlberg ...
Added
#407 Added genotyping sub-workflow.
#424 Added support for AIRR-C germline reference.
Fixed
#420 Fixed a bug in the Alakazam collapseDuplicates function.
#411 Fixed a bug in Enchantr dowse...
github.com
Changed
#170 - Updated local modules to versions topic output. (by @vagkaratzas)
#171
Updated nf-core modules and subworkflows to latest, removing all remaining ch_versions. (by @vagkaratzas)
Upd...
github.com
Snorlax is a Pokémon whose body is composed of mostly its belly. It wakes up only to eat, requiring about 400 kg of food per day before returning to its slumber, although it can also eat while it i...
Initial release.
What's Changed
FEAT: add CNVKIT + base skeleton by @maxulysse in #5
Update CNVkit/batch by @ramprasadn in #9
Add germlinecnvcaller by @ramprasadn in #10
Add optional targets argum...
What's Changed
Fusionreport Fixes (Cosmic etc pp) by @apeltzer in #815
make fasta input of star a value channel by @nvnieuwk in #816
Bump 4.1.3 by @apeltzer in #818
PR for 4.1.3 release by @apelt...
v2.3.0 "Umi budou" - [June 10th 2026]
Added
New --multi_cram option to produce a multi-query CRAM file combining all the alignments (#60).
New --multiqc_thumbs option to produce alignment thumbnai...
Fixed
PR#57 - Fix input declaration of the model file for the module: numorph3dunet to be reused for all inputs.
Remove conda batch from readme, the pipeline does not support conda.
PR#66 - Set ma...
github.com
What's Changed
back to dev by @maxulysse in #284
CHORES: Update all modules and subworkflows by @maxulysse in #287
Modules/subworkflows update by @maxulysse in #288
update modules and subworkflows...
