Pipeline release! nf-core/pathogensurveillance v1.1.0 - 1.1.0!
Surveillance of pathogens using population genomics and sequencing
Please see the changelog: https://github.com/nf-core/pathogensurveillance/releases/tag/1.1.0

#nfcore #openscience #nextflow #bioinformatics

splitting a big parquet file into chunks

read (in parallel) every chunk and write again into two different output files

#nextflow #parquet

Pipeline release! nf-core/sarek v3.8.1 - 3.8.1 - Laitaure!
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.8.1

#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/createtaxdb v2.1.0 - v2.1.0 - Gracious Goblin - [2026-02-10]!
Parallelised and automated construction of metagenomic classifier databases of different tools
Please see the changelog: https://github.com/nf-core/createtaxdb/releases/tag/2.1.0

#database #databasebuilder #metagenomicprofiling #metagenomics #profiling #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/rnavar v1.2.3 - nf-core/rnavar 1.2.3 - Yellow Hammer Head!
gatk4 RNA variant calling pipeline
Please see the changelog: https://github.com/nf-core/rnavar/releases/tag/1.2.3

#gatk4 #rna #rnaseq #variantcalling #worflow #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/sarek v3.8.0 - 3.8.0 - Sitojaure!
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.8.0

#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/proteinannotator v1.0.0 - Yellow Saiga!
Generation of sequence-level annotations for amino acid sequences
Please see the changelog: https://github.com/nf-core/proteinannotator/releases/tag/1.0.0

#annotation #proteomics #nfcore #openscience #nextflow #bioinformatics

#nextflow #parquet plugin version v0.2.2 is out!

This update introduces powerful new splitting capabilities including by, file, and count options, bringing it in line with standard Nextflow splitters as splitFasta for example.

Specifically, the file option allows you to partition large datasets into smaller chunks, enabling seamless parallel processing

Additionally, this version includes an experimental feature for reading files directly from S3

Read more at https://nextflow-io.github.io/nf-parquet/

Collecting all my posts about #nextflow #plugins in a new site

https://nextflow.incsteps.com/

More material will come in these days including creating a kubernetes cluster in Oracle cloud and linking it with Tower in only a few minutes

Super excited

After dithered images my next obsession is 'workflow managers' 🎈Yesterday night I binged some videos from #riffomonas about #reproducible research (CC248 to CC256). He used #snakemake , which looked very nice! Now I also looked up #nextflow It looks fierce!
I am going to learn one of them, and snakemake currently feels more approachable... But what do you think? Any advice? I want to use it in my #bioinformatics #pipeline s; I mainly write in R
#rstats #tidyverse
https://riffomonas.org

Pipeline release! nf-core/airrflow v5.0.0 - Tarantallegra!
B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
Please see the changelog: https://github.com/nf-core/airrflow/releases/tag/5.0.0

#airr #bcell #immcantation #immunorepertoire #repseq #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/mag v5.4.0 - mag 5.4.0 - Yellow Frog!
Assembly and binning of metagenomes
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.4.0

#annotation #assembly #binning #longreadsequencing #metagenomes #metagenomics #nanopore #nanoporesequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/hlatyping v2.2.0 - 2.2.0 - Holocron!
Precision HLA typing from next-generation sequencing data
Please see the changelog: https://github.com/nf-core/hlatyping/releases/tag/2.2.0

#dna #hla #hlatyping #immunology #optitype #personalizedmedicine #rna #nfcore #openscience #nextflow #bioinformatics

yesterday I've published #nextflow #parquet plugin version 0.2.2-edge2

a big refactor of the plugin to be aligned with others Splitters

now you can chunk a parquet file into smaller files using the `file` option, specify a batch size using `by` option, and so on

happy to see how this plugin is gaining popularity

https://nextflow-io.github.io/nf-parquet/

Reducing haystacks to needles - ViralClust: A #Nextflow pipeline to cluster viral sequences www.biorxiv.org/content/10.6... 🧬💻🧪 github.com/rnajena/vira...

Pipeline release! nf-core/nanostring v1.3.3 - v1.3.3 - 2026-01-30 - Micrometer patch 3!
An analysis pipeline for Nanostring nCounter expression data.
Please see the changelog: https://github.com/nf-core/nanostring/releases/tag/1.3.3

#nanostring #nanostringnorm #nfcore #openscience #nextflow #bioinformatics

#nextflow "Preparing for strict syntax" https://www.nextflow.io/docs/latest/strict-syntax.html

Pipeline release! nf-core/demo v1.1.0 - nf-core/demo 1.1.0 - Grammar Police!
nf-core/demo is a simple nf-core style bioinformatics pipeline for workshops and demos.
Please see the changelog: https://github.com/nf-core/demo/releases/tag/1.1.0

#demo #minimalexample #training #tutorial #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/pairgenomealign v2.2.2 - nf-core/pairgenomealign v2.2.2 – Juicy!
Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results
Please see the changelog: https://github.com/nf-core/pairgenomealign/releases/tag/2.2.2

#comparativegenomics #dotplot #genomics #last #pairwisealignment #synteny #wholegenomealignment #nfcore #openscience #nextflow #bioinformatics

Sigo sacando ratos no sé de donde y avanzando en el plugin OpenSource de #nextflow

anima ver que el número de usuarios empieza a despegar