nf-core/newsletter, September 2024

Blog posts

• Maintainers Minutes: September 2024 — Keeping you informed of the latest maintainers discussions
  30 Aug 2024 · by FriederikeHanssen

  

• Maintainers Minutes: August 2024 — Keeping you informed of the latest maintainers discussions
  14 Aug 2024 · by jfy133, FriederikeHanssen

  

New pipeline first releases 🎉

These pipelines just had their very first release.

• nf-core/denovotranscript v1.0.0 — A pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq
• nf-core/oncoanalyser v1.0.0 — A comprehensive cancer DNA/RNA analysis and reporting pipeline
• nf-core/pairgenomealign v1.0.0 — Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results

Pipeline releases

• nf-core/ampliseq v2.11.0 (5 Aug 2024)
• nf-core/demultiplex v1.5.0, v1.5.1 (20 Aug 2024)
• nf-core/mag v3.0.3 (27 Aug 2024)
• nf-core/nanostring v1.3.0 (27 Aug 2024)
• nf-core/sarek v3.4.3 (7 Aug 2024)
• nf-core/scrnaseq v2.7.1 (15 Aug 2024)

Upcoming events

• Bytesize Bytesize: Special Interest Group meta-omics — 3 Sept 2024
  <p>Daniel Lundin (Linnaeus University / Stockholm University), James Fellows Yates (HKI Jena / MPI-EVA Leipzig) and Carson J. Miller (University of Washington)</p>
• Talk #regulatory: Where do we stand and where do we want to go? — 9 Sept 2024
  <p>Round table in regulatory led by Alex Peltzer (Boehringer Ingelheim Pharma GmbH)</p>
• Bytesize Bytesize: Excalidraw — 17 Sept 2024
  <p>Phil Ewels, Seqera</p>
• Talk #animal-genomics: September Meeting — 18 Sept 2024
  <p>Guillaume Devailly (INRAE, France), Cervin Guyomar (INRAE, France), Sandrine Lagarrigue (INRAE, France)</p>
• Hackathon Bioimage Analysis Workshop - September 2024 (Tübingen) — 26 Sept 2024 – 27 Sept 2024
  <p>An in-person and online bioimage analysis workshop in Tübingen</p>
• Bytesize Bytesize: Animating subway maps — 1 Oct 2024
  <p>Maxime Garcia, Seqera</p>
• Bytesize Bytesize: Making Pipeline level tests with nf-test — 8 Oct 2024
  <p>Maxime Garcia, Seqera</p>
• Talk #regulatory - monthly meeting — 15 Oct 2024
  <p>Round table in regulatory led by Alex Peltzer (Boehringer Ingelheim Pharma GmbH)</p>
• Talk #animal-genomics: October Meeting — 16 Oct 2024
  <p>Roderic Guigó (CRG, Spain)</p>
• Hackathon Hackathon - October 2024 (Barcelona) — 28 Oct 2024 – 30 Oct 2024
  <p>An in-person hackathon held in Barcelona</p>

In case you missed it

Earlier blog posts

• A gentle introduction to nf-core/reportho — 18 Jul 2024
• nf-core/callingcards - first release! — 17 Jul 2024
• Maintainers Minutes: July 2024 — 3 Jul 2024
• Faster nf-core website builds — 3 Jul 2024
• nf-core/fastquorum - first release! — 22 Jun 2024
• Introducing nf-core office hours — 13 Jun 2024
• Maintainers Minutes: June 2024 — 7 Jun 2024

New pipelines & proposals

New pipeline repositories

• nf-core/methylarray (in development) — Process methylation data from Illumina arrays. Pre-processing, quality checks, confounder check and DMPs (differentially methylated positions) and DMRs (differentially methylated regions). Optionally estimates cell type composition and adjusts data for it.
• nf-core/troughgraph (in development) — A quantitative assessment of the underlying permafrost landscapes and, per extension, of the level of permafrost thaw in the region