# nf-core/newsletter, June 2025 2 blog posts, 1 advisory, 11 pipeline releases, 7 upcoming events. [View on the nf-core website](https://nf-co.re/newsletter/2025/06) ## Blog posts - [nf-core supports now `main` branch names](https://nf-co.re/blog/2025/switching-master-to-main) — Announcing the possibility to change a pipeline default branch to main _19 May 2025 · by mirpedrol, jfy133_ - [Maintainers Minutes: April 2025](https://nf-co.re/blog/2025/maintainers-minutes-2025-04-24) — Keeping you informed of the latest maintainers discussions _2 May 2025 · by jfy133_ ## Advisories - **HIGH** [.command.run Permission denied](https://nf-co.re/advisories/process-shell-configuration) _(Incompatibility)_ — 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/methylong](https://nf-co.re/methylong) v1.0.0 — Extract methylation calls from long reads (ONT/ PacBio) ## Pipeline releases - [nf-core/ampliseq](https://nf-co.re/ampliseq) v2.14.0 _(23 May 2025)_ - [nf-core/coproid](https://nf-co.re/coproid) v2.0.0 _(22 May 2025)_ - [nf-core/epitopeprediction](https://nf-co.re/epitopeprediction) v3.0.0 _(9 May 2025)_ - [nf-core/mag](https://nf-co.re/mag) v4.0.0 _(22 May 2025)_ - [nf-core/mhcquant](https://nf-co.re/mhcquant) v3.0.0 _(22 May 2025)_ - [nf-core/multiplesequencealign](https://nf-co.re/multiplesequencealign) v1.1.1 _(27 May 2025)_ - [nf-core/nascent](https://nf-co.re/nascent) v2.3.0 _(8 May 2025)_ - [nf-core/pairgenomealign](https://nf-co.re/pairgenomealign) v2.1.0 _(16 May 2025)_ - [nf-core/proteinfamilies](https://nf-co.re/proteinfamilies) v1.1.0, v1.1.1 _(20 May 2025)_ - [nf-core/raredisease](https://nf-co.re/raredisease) v2.5.0 _(22 May 2025)_ ## Upcoming events - **Talk** [Bytesize: nf-core/rangeland](https://nf-co.re/events/2025/bytesize_rangeland) — 10 Jun 2025 Felix Kummer, Humboldt-Universität zu Berlin - **Training** [meta-omics nf-test fest](https://nf-co.re/events/2025/sig_metaomics_nftestfest) — 11 Jun 2025 – 12 Jun 2025 Hackathon to implement nf-test in meta-omics related pipelines! - **Training** [Introduction to nf-core/airrflow](https://nf-co.re/events/2025/training_nf-core-airrflow_june) — 12 Jun 2025 Introductory practical workshop to nf-core/airrflow - **Talk** [#animal-genomics: June Meeting](https://nf-co.re/events/2025/sig_animalgenomics_jun) — 18 Jun 2025 Ángela Cánovas (Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada) - **Training** [Nextflow Training Week - June 2025](https://nf-co.re/events/2025/training-week-q2) — 23 Jun 2025 – 27 Jun 2025 Join the Nextflow Training Week in June - **Talk** [Bytesize: nf-core test-datasets](https://nf-co.re/events/2025/bytesize_nfcore_testdatasets) — 8 Jul 2025 Julian Flesch, QBiC, University Tübingen - **Talk** [#animal-genomics: July Meeting](https://nf-co.re/events/2025/sig_animalgenomics_jul) — 16 Jul 2025 Luca Fontanesi (Full Professor of animal breeding and genetics at the University of Bologna) ## In case you missed it ### Recent events - [Bytesize: nf-core/fastqrepair](https://nf-co.re/events/2025/bytesize_nfcore_fastqrepair) — 13 May 2025 (Talk) - [Hackathon - May 2025 (Boston)](https://nf-co.re/events/2025/hackathon-boston) — 13 May 2025 – 14 May 2025 (Hackathon) - [#animal-genomics: May Meeting](https://nf-co.re/events/2025/sig_animalgenomics_may) — 21 May 2025 (Talk) ### Earlier blog posts - [State of the nf-core CI](https://nf-co.re/blog/2025/state-of-nf-core-ci) — 9 Apr 2025 - [nf-core survey 2025: the results](https://nf-co.re/blog/2025/survey-results-2025) — 26 Mar 2025 - [Spring cleaning 2025](https://nf-co.re/blog/2025/springcleaning) — 20 Mar 2025 - [nf-core weekly help desk is coming to Asia-Pacific!](https://nf-co.re/blog/2025/apac-helpdesk-2025) — 10 Mar 2025 ## New pipelines & proposals ### New pipeline repositories - [nf-core/alleleexpression](https://nf-co.re/alleleexpression) _(in development)_ — 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/cellpainting](https://nf-co.re/cellpainting) _(in development)_ — null - [nf-core/longraredisease](https://nf-co.re/longraredisease) — Long read sequencing pipeline to identify variants in patients with neurodevelopmental disorders ### Pipeline proposals From [nf-core/proposals](https://github.com/nf-core/proposals/issues). - [nf-core/panoramaseq](https://github.com/nf-core/proposals/issues/20) — Accepted (#20) - [nf-core/longrnaseq](https://github.com/nf-core/proposals/issues/29) — New (#29) - [nf-core/viralmetagenome - untargeted viral genome reconstruction](https://github.com/nf-core/proposals/issues/28) — New (#28) - [nf-core/dbcan](https://github.com/nf-core/proposals/issues/27) — New (#27) - [nf-core/taxonomicfiltering](https://github.com/nf-core/proposals/issues/26) — New (#26) - [nf-core/rsvrecon](https://github.com/nf-core/proposals/issues/25) — New (#25) - [nf-core/methflow](https://github.com/nf-core/proposals/issues/24) — New (#24) - [nf-core/mitnanex](https://github.com/nf-core/proposals/issues/22) — New (#22) ### Other proposals - [New RFC: New nf-core RFC system for major initiatives](https://github.com/nf-core/proposals/issues/30) — Accepted (#30) - [New RFC: Introducing "Advisories" as a new content type for structured issue reporting](https://github.com/nf-core/proposals/issues/44) — New (#44) - [New RFC: CODEOWNER for pipelines](https://github.com/nf-core/proposals/issues/40) — New (#40) - [New RFC: `main.nf` for each nextflow script](https://github.com/nf-core/proposals/issues/39) — New (#39) --- This newsletter is brought to you by the [nf-core](https://nf-co.re) community.