nf-core/newsletter, February 2023

Advisories

• LOW Trimming parameters ignored in RNA-seq pipeline 3.10 (Known Regression) — The clip parameters for read trimming remain without affect for that pipeline version

New pipeline first releases 🎉

These pipelines just had their very first release.

• nf-core/differentialabundance v1.0.0, v1.0.1 — Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

Pipeline releases

• nf-core/demultiplex v1.1.0 (23 Jan 2023)
• nf-core/hic v2.0.0 (21 Jan 2023)
• nf-core/isoseq v1.1.2 (12 Jan 2023)
• nf-core/rnaseq v3.10.1 (5 Jan 2023)
• nf-core/sarek v3.1.2 (5 Jan 2023)

Upcoming events

• Talk Bytesize: nf-core/pre-commit — 7 Feb 2023
  Matthias Hörtenhuber, Scilifelab Data Centre, Sweden
• Talk Bytesize: nf-core/crisprseq — 14 Feb 2023
  Júlia Mir (QBiC, Tübingen University) and Marta Sanvincente (Pompeu Fabra University, Barcelona)
• Talk Bytesize: variantcatalogue — 21 Feb 2023
  Solenne Correard, University of British Columbia, Vancouver, Canada
• Talk Bytesize: nf-core/mag — 28 Feb 2023
  Sabrina Krakau - University Tübingen, QBiC
• Talk Bytesize: nf-core modules patch — 7 Mar 2023
  Phil Ewels - Seqera Labs
• Training nf-core Training - March 2023 — 13 Mar 2023 – 16 Mar 2023
  A set of global online Nextflow and nf-core training events
• Talk Bytesize: nf-core/hgtseq — 21 Mar 2023
  Francesco Lescai - Department of Biology and Biotechnology, University of Pavia
• Hackathon Hackathon - March 2023 (Online) — 27 Mar 2023 – 29 Mar 2023
  A virtual hackathon with local gatherings to develop nf-core together

In case you missed it

Recent events

• Bytesize: nf-core/taxprofiler — 17 Jan 2023 (Talk )
• Bytesize: nf-core/funcscan — 24 Jan 2023 (Talk )
• Bytesize: transcripts of bytesize talks — 31 Jan 2023 (Talk )

New pipelines & proposals

New pipeline repositories

• nf-core/pathogensurveillance — Surveillance of pathogens using population genomics and sequencing
• nf-core/viralmetagenome — A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.