Looks useful: github.com/nf-core/path...
June 27, 2025 at 6:20 PM
Looks useful: github.com/nf-core/path...
Cluster-efficient pangenome graph construction with nf-core/pangenome https://academic.oup.com/bioinformatics/article/40/11/btae609/7821182 🧬🖥️🧪 https://github.com/nf-core/pangenome
November 16, 2024 at 4:44 PM
Cluster-efficient pangenome graph construction with nf-core/pangenome https://academic.oup.com/bioinformatics/article/40/11/btae609/7821182 🧬🖥️🧪 https://github.com/nf-core/pangenome
PathogenSurveillance: an automated pipeline for population genomic analyses and pathogen identification www.biorxiv.org/content/10.1...
Code: github.com/nf-core/path...
Nextflow nf-core pipeline: nf-co.re/pathogensurv...
Code: github.com/nf-core/path...
Nextflow nf-core pipeline: nf-co.re/pathogensurv...
November 2, 2025 at 9:58 PM
PathogenSurveillance: an automated pipeline for population genomic analyses and pathogen identification www.biorxiv.org/content/10.1...
Code: github.com/nf-core/path...
Nextflow nf-core pipeline: nf-co.re/pathogensurv...
Code: github.com/nf-core/path...
Nextflow nf-core pipeline: nf-co.re/pathogensurv...
scnanoseq nf-co.re/scrnaseq: an nf-core [Nextflow] pipeline for Oxford Nanopore single-cell RNA-sequencing www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/nf-core/scna...
April 11, 2025 at 8:00 PM
scnanoseq nf-co.re/scrnaseq: an nf-core [Nextflow] pipeline for Oxford Nanopore single-cell RNA-sequencing www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/nf-core/scna...
Build common reference indexes with Nextflow @nf-co.re nf-core/references https://github.com/nf-core/references 🧬🖥️🧪
December 30, 2024 at 12:06 PM
Build common reference indexes with Nextflow @nf-co.re nf-core/references https://github.com/nf-core/references 🧬🖥️🧪
nf-core/variantbenchmarking v1.0.0: Nextflow pipeline to evaluate and validate the accuracy of variant calling methods https://github.com/nf-core/variantbenchmarking 🧬🖥️🧪
February 24, 2025 at 10:31 AM
nf-core/variantbenchmarking v1.0.0: Nextflow pipeline to evaluate and validate the accuracy of variant calling methods https://github.com/nf-core/variantbenchmarking 🧬🖥️🧪
One of my favorite talks at the @nextflow.io summit was @kenibrewer.bsky.social's talk on how to NOT contribute to nf-core (using nf-core in your organization). He wrote a nice post on the @nf-co.re blog on building an nf-core style modules library for your organization seqera.io/blog/buildin...
Building an nf-core style modules library for your organization | Seqera
If you would like to bring nf-core’s approach to enabling code within your own organization, you can!
seqera.io
January 2, 2025 at 1:30 PM
One of my favorite talks at the @nextflow.io summit was @kenibrewer.bsky.social's talk on how to NOT contribute to nf-core (using nf-core in your organization). He wrote a nice post on the @nf-co.re blog on building an nf-core style modules library for your organization seqera.io/blog/buildin...
nf-core/detaxizer nf-co.re/detaxizer: A Benchmarking Study for Decontamination from Human Sequences www.biorxiv.org/content/10.1... 🧬🖥️🧪 nextflow github.com/nf-core/deta...
March 31, 2025 at 10:01 AM
nf-core/detaxizer nf-co.re/detaxizer: A Benchmarking Study for Decontamination from Human Sequences www.biorxiv.org/content/10.1... 🧬🖥️🧪 nextflow github.com/nf-core/deta...
Oh boy - our new ancient DNA module is available for nf-core/mag! Robustly and reproducibly reconstruct ancient metagenome-assembled genomes (MAGs) using our new nf-core/mag tooling!
doi.org/10.1371/jour...
doi.org/10.1371/jour...
August 13, 2026 at 3:52 AM
Oh boy - our new ancient DNA module is available for nf-core/mag! Robustly and reproducibly reconstruct ancient metagenome-assembled genomes (MAGs) using our new nf-core/mag tooling!
doi.org/10.1371/jour...
doi.org/10.1371/jour...
Pipeline release! nf-core/scrnaseq v2.4.1 - nf-core/scrnaseq 2.4.1!
Please see the changelog: https://github.com/nf-core/scrnaseq/releases/tag/2.4.1
Please see the changelog: https://github.com/nf-core/scrnaseq/releases/tag/2.4.1
October 2, 2023 at 12:18 PM
Pipeline release! nf-core/scrnaseq v2.4.1 - nf-core/scrnaseq 2.4.1!
Please see the changelog: https://github.com/nf-core/scrnaseq/releases/tag/2.4.1
Please see the changelog: https://github.com/nf-core/scrnaseq/releases/tag/2.4.1
nf-core/pacvar (nf-co.re/pacvar/): a [Nextflow] pipeline for analyzing longread PacBio whole genome and repeat expansion sequencing data academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/nf-core/pacvar
March 19, 2025 at 12:03 PM
nf-core/pacvar (nf-co.re/pacvar/): a [Nextflow] pipeline for analyzing longread PacBio whole genome and repeat expansion sequencing data academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/nf-core/pacvar
November 14, 2024 at 1:48 PM
nf-core/proteinfamilies: A scalable [Nextflow] pipeline for the generation of protein families www.biorxiv.org/content/10.1... 🧬🖥️🧪
Code (MIT): github.com/nf-core/prot...
Docs/launch: nf-co.re/proteinfamil...
Code (MIT): github.com/nf-core/prot...
Docs/launch: nf-co.re/proteinfamil...
August 17, 2025 at 10:10 AM
nf-core/proteinfamilies: A scalable [Nextflow] pipeline for the generation of protein families www.biorxiv.org/content/10.1... 🧬🖥️🧪
Code (MIT): github.com/nf-core/prot...
Docs/launch: nf-co.re/proteinfamil...
Code (MIT): github.com/nf-core/prot...
Docs/launch: nf-co.re/proteinfamil...
Big update for nf-core Proteinfold for protein people… check out v2. Great team effort! nf-co.re/proteinfold/...
April 1, 2026 at 2:46 AM
Big update for nf-core Proteinfold for protein people… check out v2. Great team effort! nf-co.re/proteinfold/...
⏳ 17 days until the Barcelona nf-core Hackathon! Join one of the existing projects, or bring your own! Today's project spotlight ⬇️
⚒️ Project → nf-core/spatialaxe improvements
🧑💻 Project Lead → Florian Heyl, @cnag-eu.bsky.social
🔗 Project Link → hubs.la/Q04ypPWK0
⚒️ Project → nf-core/spatialaxe improvements
🧑💻 Project Lead → Florian Heyl, @cnag-eu.bsky.social
🔗 Project Link → hubs.la/Q04ypPWK0
September 28, 2026 at 9:47 AM
⏳ 17 days until the Barcelona nf-core Hackathon! Join one of the existing projects, or bring your own! Today's project spotlight ⬇️
⚒️ Project → nf-core/spatialaxe improvements
🧑💻 Project Lead → Florian Heyl, @cnag-eu.bsky.social
🔗 Project Link → hubs.la/Q04ypPWK0
⚒️ Project → nf-core/spatialaxe improvements
🧑💻 Project Lead → Florian Heyl, @cnag-eu.bsky.social
🔗 Project Link → hubs.la/Q04ypPWK0
Pipeline release! nf-core/stableexpression vv1.0.0 - nf-core/stableexpression v1.0.0 - Prunus persica!
Please see the changelog: https://github.com/nf-core/stableexpression/releases/tag/v1.0.0
Please see the changelog: https://github.com/nf-core/stableexpression/releases/tag/v1.0.0
Release nf-core/stableexpression v1.0.0 - Prunus persica · nf-core/stableexpression
Initial release of the nf-core/stableexpression pipeline.
The full commit history is available here.
github.com
September 22, 2026 at 11:01 AM
Pipeline release! nf-core/stableexpression vv1.0.0 - nf-core/stableexpression v1.0.0 - Prunus persica!
Please see the changelog: https://github.com/nf-core/stableexpression/releases/tag/v1.0.0
Please see the changelog: https://github.com/nf-core/stableexpression/releases/tag/v1.0.0
Pipeline release! nf-core/denovotranscript v1.1.0 - nf-core/denovotranscript v1.1.0!
Please see the changelog: https://github.com/nf-core/denovotranscript/releases/tag/1.1.0
Please see the changelog: https://github.com/nf-core/denovotranscript/releases/tag/1.1.0
November 29, 2024 at 12:26 AM
Pipeline release! nf-core/denovotranscript v1.1.0 - nf-core/denovotranscript v1.1.0!
Please see the changelog: https://github.com/nf-core/denovotranscript/releases/tag/1.1.0
Please see the changelog: https://github.com/nf-core/denovotranscript/releases/tag/1.1.0
Pipeline release! nf-core/scrnaseq v4.0.0 - 4.0.0!
Please see the changelog: https://github.com/nf-core/scrnaseq/releases/tag/4.0.0
Please see the changelog: https://github.com/nf-core/scrnaseq/releases/tag/4.0.0
March 11, 2025 at 8:05 AM
Pipeline release! nf-core/scrnaseq v4.0.0 - 4.0.0!
Please see the changelog: https://github.com/nf-core/scrnaseq/releases/tag/4.0.0
Please see the changelog: https://github.com/nf-core/scrnaseq/releases/tag/4.0.0
If you're analysing Cut&Run or Cut&Tag data here's a nf-core NextFlow pipeline to simplify and standardise data processing
joss.theoj.org/papers/10.21...
joss.theoj.org/papers/10.21...
nf-core/cutandrun: A Nextflow pipeline for the analysis of CUT&RUN, CUT&Tag and TIP-seq datasets
Hodgetts et al., (2026). nf-core/cutandrun: A Nextflow pipeline for the analysis of CUT&RUN, CUT&Tag and TIP-seq datasets. Journal of Open Source Software, 11(119), 9672, https://doi.org/10.21...
joss.theoj.org
March 17, 2026 at 11:52 AM
If you're analysing Cut&Run or Cut&Tag data here's a nf-core NextFlow pipeline to simplify and standardise data processing
joss.theoj.org/papers/10.21...
joss.theoj.org/papers/10.21...
nf-core/genomeqc is finally on bioRxiv,, a best-practice #Nextflow pipeline for comparing #genome & assembly quality, grown out of the 2024 @nf-co.re Barcelona hackathon with Fernando Duarte, @stephenturner.us and more.
August 22, 2026 at 8:59 AM
nf-core/genomeqc is finally on bioRxiv,, a best-practice #Nextflow pipeline for comparing #genome & assembly quality, grown out of the 2024 @nf-co.re Barcelona hackathon with Fernando Duarte, @stephenturner.us and more.
I spent most of my time at the 2024 #Nextflow @nf-co.re hackathon working on genomeqc. Happy to see our preprint finally published:
nf-core/genomeqc: a best-practice pipeline for comparing genome and assembly quality: www.biorxiv.org/content/10.6... 🧬💻🧪 github.com/nf-core/geno...
nf-core/genomeqc: a best-practice pipeline for comparing genome and assembly quality: www.biorxiv.org/content/10.6... 🧬💻🧪 github.com/nf-core/geno...
August 21, 2026 at 4:09 PM
I spent most of my time at the 2024 #Nextflow @nf-co.re hackathon working on genomeqc. Happy to see our preprint finally published:
nf-core/genomeqc: a best-practice pipeline for comparing genome and assembly quality: www.biorxiv.org/content/10.6... 🧬💻🧪 github.com/nf-core/geno...
nf-core/genomeqc: a best-practice pipeline for comparing genome and assembly quality: www.biorxiv.org/content/10.6... 🧬💻🧪 github.com/nf-core/geno...
A #methods paper for #MetagenomicsMonday! 🦠🧬💻
This new primer and #protocol provides practical guidance for assembling and validating #ancient #microbial #genomes. It introduces dedicated #aDNA support in #nf-core/mag.
journals.plos.org/ploscompbiol...
#SPAAM #Metagenomics #Bioinformatics
This new primer and #protocol provides practical guidance for assembling and validating #ancient #microbial #genomes. It introduces dedicated #aDNA support in #nf-core/mag.
journals.plos.org/ploscompbiol...
#SPAAM #Metagenomics #Bioinformatics
De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag
Author summary Advancements in genomic sequencing analyses are increasingly allowing researchers to reconstruct the genomes of microbial ‘dark matter’—those microbial species that are difficult to…
journals.plos.org
September 21, 2026 at 11:08 AM
A #methods paper for #MetagenomicsMonday! 🦠🧬💻
This new primer and #protocol provides practical guidance for assembling and validating #ancient #microbial #genomes. It introduces dedicated #aDNA support in #nf-core/mag.
journals.plos.org/ploscompbiol...
#SPAAM #Metagenomics #Bioinformatics
This new primer and #protocol provides practical guidance for assembling and validating #ancient #microbial #genomes. It introduces dedicated #aDNA support in #nf-core/mag.
journals.plos.org/ploscompbiol...
#SPAAM #Metagenomics #Bioinformatics
Pipeline release! nf-core/rnaseq v3.18.0 - nf-core/rnaseq v3.18.0 - Lithium Lynx!
Please see the changelog: https://github.com/nf-core/rnaseq/releases/tag/3.18.0
Please see the changelog: https://github.com/nf-core/rnaseq/releases/tag/3.18.0
December 20, 2024 at 4:54 PM
Pipeline release! nf-core/rnaseq v3.18.0 - nf-core/rnaseq v3.18.0 - Lithium Lynx!
Please see the changelog: https://github.com/nf-core/rnaseq/releases/tag/3.18.0
Please see the changelog: https://github.com/nf-core/rnaseq/releases/tag/3.18.0
Pipeline release! nf-core/funcprofiler v1.0.0 - funcprofiler version 1.0.0!
Please see the changelog: https://github.com/nf-core/funcprofiler/releases/tag/1.0.0
Please see the changelog: https://github.com/nf-core/funcprofiler/releases/tag/1.0.0
Release funcprofiler version 1.0.0 · nf-core/funcprofiler
Initial release! funcprofiler can handle single or paired-end short read data, and can run the following tools:
HUMANnN
RGI
mifaser
fmh-funprofiler
github.com
September 21, 2026 at 3:26 PM
Pipeline release! nf-core/funcprofiler v1.0.0 - funcprofiler version 1.0.0!
Please see the changelog: https://github.com/nf-core/funcprofiler/releases/tag/1.0.0
Please see the changelog: https://github.com/nf-core/funcprofiler/releases/tag/1.0.0