The last blog post I wrote was about Life Science Support on HPC clusters. Honestly? It was more of a rant. Not a good blog post.

So, someone suggested I delete it, which I did. It took me a long time to recover. Now, I have re-written this blog post. I think it is better. I weighted every phrase. It still has some rant flavour.

Here it is: https://blogs.fediscience.org/rupture-de-catenaire/2025/12/15/empowering-life-scientists-what-hpc-support-should-look-like/

The upcoming articles will have more of an example character. But I still will not be able to update on a regular basis.

#Bioinformatics #HPC #ReproducibleComputing #Snakemake #Nextflow

Pipeline release! nf-core/pixelator v2.3.0 - nf-core/pixelator 2.3.0!
Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)
Please see the changelog: https://github.com/nf-core/pixelator/releases/tag/2.3.0

#molecularpixelation #pixelator #pixelgentechnologies #proteins #singlecell #singlecellomics #nfcore #openscience #nextflow #bioinformatics

playing with #nextflow plugins and #gephi / gexf.

(made with gephisto: https://jacomyma.github.io/gephisto/ )

#visualization

Pipeline release! nf-core/methylseq v4.2.0 - Tapus Maximus!
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth MethylDackel
Please see the changelog: https://github.com/nf-core/methylseq/releases/tag/4.2.0

#bisulfitesequencing #dnamethylation #emseq #epigenome #epigenomics #methylseq #pbat #rrbs #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/rnaseq v3.22.2 - nf-core/rnaseq v3.22.2 - Perfect Palladium Penguin!
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Please see the changelog: https://github.com/nf-core/rnaseq/releases/tag/3.22.2

#rna #rnaseq #nfcore #openscience #nextflow #bioinformatics

- el executor nf-nomad de #nextflow empieza a ganar popularidad con casi 1000 descargas y (creo) es el más usado de los executors "no oficiales"

- el plugin #parquet de #nextflow ya está por las 500 descargas. Espero que el año que viene sea el del plugin de #aspera , creado este Q4

y no sólo de proyectos desplegados vive el hombre:

2/3

🎉 Huge shout out to everyone who instructed and participated in yesterday's online Meta-*omics #Nextflow Pipeline Community Exhibition Day!

🧑‍🏫 Over 9 hours, we had 15 different pipelines demo'd by their lead developers, and giving an international cohort of participants hands-on experience on running diverse pipelines spanning #metataxonomics, #metagenomics, #metatranscriptomics, and #metaproteomics, as well as a crash-course on the different ways to configure Nextflow pipelines.

[🧵 1/3]

Pipeline release! nf-core/sarek v3.7.1 - 3.7.1 - Buollámtjåhkka!
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/3.7.1

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

Pipeline release! nf-core/oncoanalyser v2.3.0 - 2.3.0 - Spotted Nightjar!
A comprehensive cancer DNA/RNA analysis and reporting pipeline
Please see the changelog: https://github.com/nf-core/oncoanalyser/releases/tag/2.3.0

#cancer #clinical #dna #exome #ngs #panel #rna #targeted #wgs #wigits #wts #nfcore #openscience #nextflow #bioinformatics

David Condon just released a #NextFlow/ #snakemame pipeline/logger alternative in #Perl:

https://metacpan.org/pod/SimpleFlow

which should make debugging and running very complex #pipelines much easier.

Pipeline release! nf-core/rnaseq v3.22.1 - nf-core/rnaseq v3.22.1 - Polished Palladium Penguin!
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Please see the changelog: https://github.com/nf-core/rnaseq/releases/tag/3.22.1

#rna #rnaseq #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/viralmetagenome v1.0.1 - 1.0.1 - Khaki Quail!
A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
Please see the changelog: https://github.com/nf-core/viralmetagenome/releases/tag/1.0.1

#epidemiology #fastq #ngs #viralmetagenomics #virology #virusgenomes #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/mag v5.3.0 - mag 5.3.0 - Rainbow Rattlesnake!
Assembly and binning of metagenomes
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.3.0

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

Pipeline release! nf-core/rnavar v1.2.2 - nf-core/rnavar 1.2.2 - Gray Red Tail!
gatk4 RNA variant calling pipeline
Please see the changelog: https://github.com/nf-core/rnavar/releases/tag/1.2.2

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

David Condon just released a #NextFlow/ #snakemame pipeline/logger alternative in #Perl: metacpan.org/pod/SimpleFlow which should make debugging and running very complex #pipelines much easier.

Client Challenge

David Condon just released a #NextFlow/ #snakemame pipeline/logger alternative in #Perl:

https://metacpan.org/pod/SimpleFlow

which should make debugging and running very complex #pipelines much easier.

David Condon just released a #NextFlow/ #snakemame pipeline/logger alternative in #Perl:

https://metacpan.org/pod/SimpleFlow

which should make debugging and running very complex #pipelines much easier.

Pipeline release! nf-core/sarek v3.7.0 - 3.7.0 - Saltoluokta!
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/3.7.0

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

🧑‍💻 Need help with #nfcore #nextflow #bioinformatics pipelines, running or developing?

We are merging the 🌍 Eur/M.E./Afr and the 🌎 Americas weekly helpdesk.

Please join our nf-core maintainers, this Thursday at 14:30 CET | 08:30 ET on https://play.workadventu.re/@/nf-core/nf-core/office

Pipeline release! nf-core/variantbenchmarking v1.4.0 - Thin Yasar!
Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research
Please see the changelog: https://github.com/nf-core/variantbenchmarking/releases/tag/1.4.0

#benchmark #smallvariants #structuralvariants #variantcalling #nfcore #openscience #nextflow #bioinformatics