nf-core/newsletter, July 2022

New pipeline first releases 🎉

These pipelines just had their very first release.

• nf-core/circdna v1.0.0, v1.0.1 — Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.
• nf-core/isoseq v1.0.0 — Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.
• nf-core/rnavar v1.0.0 — gatk4 RNA variant calling pipeline

Pipeline releases

• nf-core/airrflow v2.2.0 (3 Jun 2022)
• nf-core/cutandrun v2.0 (8 Jun 2022)
• nf-core/mag v2.2.0 (14 Jun 2022)
• nf-core/nanoseq v3.0.0 (20 Jun 2022)
• nf-core/sarek v2.7.2 (10 Jun 2022)
• nf-core/scrnaseq v2.0.0 (17 Jun 2022)

Upcoming events

• Talk Bytesize: DSL2 Coding style recommendations (Part 1) — 5 Jul 2022
  Maxime Garcia - Barncancerfonden, Stockholm, Sweden
• Talk Bytesize: nf-core/inkscape and tube map diagrams — 12 Jul 2022
  James Fellows Yates - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
• Talk Bytesize: Bactopia & using nf-core components in non-nf-core pipelines — 19 Jul 2022
  Robert A Petit III - Wyoming Public Health Lab, USA
• Talk Bytesize: nf-core/chipseq — 26 Jul 2022
  Jose Espinosa-Carrasco - Center for Genomic Regulation, Barcelona

In case you missed it

Recent events

• Bytesize: nf-core/viralrecon — 7 Jun 2022 (Talk )
• Bytesize: gitpod.io — 14 Jun 2022 (Talk )
• Bytesize: nf-core/nanoseq — 21 Jun 2022 (Talk )

New pipelines & proposals

New pipeline repositories

• nf-core/isoseq — Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.
• nf-core/rnadnavar (in development) — Pipeline for RNA and DNA integrated analysis for somatic mutation detection