Newsletter - June 2025
nf-core community newsletter for June 2025
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2 blog posts, 1 advisory, 11 pipeline releases, 7 upcoming events.
 1st June2025 |
Blog posts
nf-core supports now `main` branch names
Announcing the possibility to change a pipeline default branch to main
19 May 2025 · by mirpedrol, jfy133
Announcing the possibility to change a pipeline default branch to main
19 May 2025 · by mirpedrol, jfy133
Maintainers Minutes: April 2025
Keeping you informed of the latest maintainers discussions
2 May 2025 · by jfy133
Keeping you informed of the latest maintainers discussions
2 May 2025 · by jfy133
Advisories
| highIncompatibility .command.run Permission denied Nextflow versions after 24.10.6 are incompatible with certain nf-core pipelines published in 2024 and early 2025. |
New pipeline first releases! 🎉
These pipelines just had their very first release.
| nf-core/methylongv1.0.0 Extract methylation calls from long reads (ONT/ PacBio) |
Pipeline releases
Upcoming events
| TalkBytesize: nf-core/rangeland | 10 Jun 2025 |
| Felix Kummer, Humboldt-Universität zu Berlin | |
| Trainingmeta-omics nf-test fest | 11 Jun 2025 – 12 Jun 2025 |
| Hackathon to implement nf-test in meta-omics related pipelines! | |
| TrainingIntroduction to nf-core/airrflow | 12 Jun 2025 |
| Introductory practical workshop to nf-core/airrflow | |
| Talk#animal-genomics: June Meeting | 18 Jun 2025 |
| Ángela Cánovas (Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada) | |
| TrainingNextflow Training Week - June 2025 | 23 Jun 2025 – 27 Jun 2025 |
| Join the Nextflow Training Week in June | |
| TalkBytesize: nf-core test-datasets | 8 Jul 2025 |
| Julian Flesch, QBiC, University Tübingen | |
| Talk#animal-genomics: July Meeting | 16 Jul 2025 |
| Luca Fontanesi (Full Professor of animal breeding and genetics at the University of Bologna) | |
In case you missed it
| State of the nf-core CI 9 Apr 2025 |  |
| nf-core survey 2025: the results 26 Mar 2025 |  |
| Spring cleaning 2025 20 Mar 2025 |  |
New pipelines & proposals
Proposals from nf-core/proposals.
nf-core/alleleexpressionNew repo
Alleleexpression is a nf-core pipeline for allele-specific expression (ASE) analysis using STAR-WASP for alignment, UMI-tools for deduplication, and phaser for haplotype phasing and ASE detection.
Alleleexpression is a nf-core pipeline for allele-specific expression (ASE) analysis using STAR-WASP for alignment, UMI-tools for deduplication, and phaser for haplotype phasing and ASE detection.
nf-core/longrarediseaseNew repo
Long read sequencing pipeline to identify variants in patients with neurodevelopmental disorders
Long read sequencing pipeline to identify variants in patients with neurodevelopmental disorders
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