nf-core/newsletter, April 2023

New pipeline first releases 🎉

These pipelines just had their very first release.

• nf-core/taxprofiler v1.0.0 — Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
• nf-core/viralintegration v0.1.0 — Analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach.

Pipeline releases

• nf-core/airrflow v3.0 (20 Mar 2023)
• nf-core/ampliseq v2.5.0 (2 Mar 2023)
• nf-core/circdna v1.0.2 (9 Mar 2023)
• nf-core/cutandrun v3.1 (10 Mar 2023)
• nf-core/differentialabundance v1.1.1 (3 Mar 2023)
• nf-core/epitopeprediction v2.2.0, v2.2.1 (17 Mar 2023)
• nf-core/isoseq v1.1.3, v1.1.4 (13 Mar 2023)
• nf-core/mag v2.3.0 (2 Mar 2023)
• nf-core/nanoseq v3.1.0 (10 Mar 2023)
• nf-core/rnafusion v2.2.0 (13 Mar 2023)
• nf-core/rnaseq v3.11.0, v3.11.1 (31 Mar 2023)
• nf-core/scrnaseq v2.2.0 (20 Mar 2023)
• nf-core/viralrecon v2.6.0 (23 Mar 2023)

Upcoming events

• Talk Bytesize: HackMD and reveal.js — 18 Apr 2023
  Maxime Garcia, Seqera Labs
• Talk Bytesize: training translations — 25 Apr 2023
  Marcel Ribeiro-Dantas, Seqera Labs
• Talk Bytesize: Converting Python scripts into packages for PyPI, Bioconda & Biocontainers — 2 May 2023
  Phil Ewels - Seqera Labs
• Talk Bytesize: Experiences in the nf-core Mentoring Program — 9 May 2023
  Mariana Guilardi (Federal University of Sao Paulo, UNIFESP) and Alyssa Briggs (The University of Texas at Dallas)
• Talk Bytesize: nf-core community survey 2023 — 16 May 2023
  Christopher Hakkaart - Seqera Labs
• Talk Bytesize: Workflow safety and immutable objects — 23 May 2023
  Rob Syme, Seqera Labs
• Talk Bytesize: nf-core/quantms — 30 May 2023
  Julianus Pfeuffer (Zuse Institute Berlin) and Yasset Perez Riverol (EMBL-EBI)

In case you missed it

Recent events

• Bytesize: nf-core modules patch — 7 Mar 2023 (Talk )
• nf-core Training - March 2023 — 13 Mar 2023 – 16 Mar 2023 (Training )
• Bytesize: nf-core/hgtseq — 21 Mar 2023 (Talk )
• Hackathon - March 2023 (Online) — 27 Mar 2023 – 29 Mar 2023 (Hackathon )

Earlier advisories

• LOW Trimming parameters ignored in RNA-seq pipeline 3.10 — 13 Jan 2023

New pipelines & proposals

New pipeline repositories

• nf-core/spinningjenny (in development) — Pipeline for simulating the first industrial revolution using Agent Based Models.