#nextflow — Public Fediverse posts

Pipeline release! nf-core/sarek v3.10.0 - 3.10.0 - Aktse!
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/3.10.0

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

Pipeline release! nf-core/sarek v3.10.0 - 3.10.0 - Aktse!
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/3.10.0

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

Pipeline release! nf-core/seqinspector v1.1.1 - nf-core/seqinspector 1.1.1 - Cindy Mackenzie!
Dedicated QC-only pipeline for sequencing data. The pipeline will run a (potentially large) set of QC tools and can output global and group specific Multiqc reports. The pipeline is targeting core facilities or research groups with larger sequencing throughput.
Please see the changelog: https://github.com/nf-core/seqinspector/releases/tag/1.1.1

#genomics #qualitycontrol #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/seqinspector v1.1.1 - nf-core/seqinspector 1.1.1 - Cindy Mackenzie!
Dedicated QC-only pipeline for sequencing data. The pipeline will run a (potentially large) set of QC tools and can output global and group specific Multiqc reports. The pipeline is targeting core facilities or research groups with larger sequencing throughput.
Please see the changelog: https://github.com/nf-core/seqinspector/releases/tag/1.1.1

#genomics #qualitycontrol #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/magmap v1.2.0 - nf-core/magmap v1.2.0!
Best-practice analysis pipeline for mapping reads to a (large) collections of genomes
Please see the changelog: https://github.com/nf-core/magmap/releases/tag/1.2.0

#nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/magmap v1.2.0 - nf-core/magmap v1.2.0!
Best-practice analysis pipeline for mapping reads to a (large) collections of genomes
Please see the changelog: https://github.com/nf-core/magmap/releases/tag/1.2.0

#nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/proteinfamilies v2.5.0 - Zinc Heron!
Generation and updating of protein families
Please see the changelog: https://github.com/nf-core/proteinfamilies/releases/tag/2.5.0

#metagenomics #proteinfamilies #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/proteinfamilies v2.5.0 - Zinc Heron!
Generation and updating of protein families
Please see the changelog: https://github.com/nf-core/proteinfamilies/releases/tag/2.5.0

#metagenomics #proteinfamilies #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/lsmquant v1.0.3 - 1.0.3 - Excited Squid!
A pipeline for processing and analysis of light-sheet microscopy images.
Please see the changelog: https://github.com/nf-core/lsmquant/releases/tag/1.0.3

#3dunet #imageanalysis #imageprocessing #lightsheetmicrocopy #segmentation #stitching #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/lsmquant v1.0.3 - 1.0.3 - Excited Squid!
A pipeline for processing and analysis of light-sheet microscopy images.
Please see the changelog: https://github.com/nf-core/lsmquant/releases/tag/1.0.3

#3dunet #imageanalysis #imageprocessing #lightsheetmicrocopy #segmentation #stitching #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/spatialaxe v1.0.1 - 1.0.1!
A bioinformatics best-practice processing and quality control pipeline for Xenium and Artera data
Please see the changelog: https://github.com/nf-core/spatialaxe/releases/tag/1.0.1

#10xgenomics #atera #imageprocessing #spatial #spatialdataanalysis #spatialtranscriptomics #transcriptomics #xenium #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/spatialaxe v1.0.1 - 1.0.1!
A bioinformatics best-practice processing and quality control pipeline for Xenium and Artera data
Please see the changelog: https://github.com/nf-core/spatialaxe/releases/tag/1.0.1

#10xgenomics #atera #imageprocessing #spatial #spatialdataanalysis #spatialtranscriptomics #transcriptomics #xenium #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/seqsubmit v1.0.0 - 1.0.0!
nf-core pipeline for data submission to ENA
Please see the changelog: https://github.com/nf-core/seqsubmit/releases/tag/1.0.0

#nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/seqsubmit v1.0.0 - 1.0.0!
nf-core pipeline for data submission to ENA
Please see the changelog: https://github.com/nf-core/seqsubmit/releases/tag/1.0.0

#nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/phyloplace v2.1.0 - v2.1.0 - 2026-08-03!
nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.
Please see the changelog: https://github.com/nf-core/phyloplace/releases/tag/2.1.0

#evolution #evolutionarytree #phylogeneticplacement #phylogenetics #sequenceclassification #taxonomyassignment #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/phyloplace v2.1.0 - v2.1.0 - 2026-08-03!
nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.
Please see the changelog: https://github.com/nf-core/phyloplace/releases/tag/2.1.0

#evolution #evolutionarytree #phylogeneticplacement #phylogenetics #sequenceclassification #taxonomyassignment #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/mag v5.5.0 - mag 5.5.0 - Purple Penguin!
Assembly and binning of metagenomes
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.5.0

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

Pipeline release! nf-core/mag v5.5.0 - mag 5.5.0 - Purple Penguin!
Assembly and binning of metagenomes
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.5.0

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

nf-core/tools - 4.1.0

https://nf-co.re/blog/2026/tools-4_1_0

#nextflow #nfcore

nf-core/tools - 4.1.0

https://nf-co.re/blog/2026/tools-4_1_0

#nextflow #nfcore

Just published version 0.1.0-edge5 of my Nextflow plugin `nf-aspera`—now with full Linux and Mac support! 🚀

Next step: write a blog post detailing the updates.

Spending my vacation downtime getting back into it and keeping the project moving.

#Nextflow #Bioinformatics #OpenSource

https://nextflow.incsteps.com/plugins/nf-aspera.html

Just published version 0.1.0-edge5 of my Nextflow plugin `nf-aspera`—now with full Linux and Mac support! 🚀

Next step: write a blog post detailing the updates.

Spending my vacation downtime getting back into it and keeping the project moving.

#Nextflow #Bioinformatics #OpenSource

https://nextflow.incsteps.com/plugins/nf-aspera.html

@LostTransposon Has probado a ponerlo en el canal de slack de #Nextflow ?

@LostTransposon Has probado a ponerlo en el canal de slack de #Nextflow ?

#biostars Forum:AI for bioinformatics pipeline development. Is it a good idea? https://www.biostars.org/p/9621061/

#ai #bioinformatics #workflow #pipeline #snakemake #nextflow

#biostars Forum:AI for bioinformatics pipeline development. Is it a good idea? https://www.biostars.org/p/9621061/

#ai #bioinformatics #workflow #pipeline #snakemake #nextflow

A #nextflow orchestra of CPUs for a Friday night

A #nextflow orchestra of CPUs for a Friday night

Pipeline release! nf-core/pairgenomealign v3.0.2 - nf-core/pairgenomealign v3.0.2 – Tokoroten shiki!
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/3.0.2

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

Pipeline release! nf-core/pairgenomealign v3.0.2 - nf-core/pairgenomealign v3.0.2 – Tokoroten shiki!
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/3.0.2

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

Pipeline release! nf-core/pixelator v5.0.0 - nf-core/pixelator 5.0.0!
Pipeline to generate Proximity Network Assay data with Pixelator (Pixelgen Technologies AB)
Please see the changelog: https://github.com/nf-core/pixelator/releases/tag/5.0.0

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

Pipeline release! nf-core/pixelator v5.0.0 - nf-core/pixelator 5.0.0!
Pipeline to generate Proximity Network Assay data with Pixelator (Pixelgen Technologies AB)
Please see the changelog: https://github.com/nf-core/pixelator/releases/tag/5.0.0

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

Pipeline release! nf-core/sopa v1.0.0 - v1.0.0 - [2026-07-15]!
Nextflow version of Sopa - spatial omics pipeline and analysis
Please see the changelog: https://github.com/nf-core/sopa/releases/tag/1.0.0

#segmentation #spatialomics #spatialproteomics #spatialtranscriptomics #spatialdata #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/sopa v1.0.0 - v1.0.0 - [2026-07-15]!
Nextflow version of Sopa - spatial omics pipeline and analysis
Please see the changelog: https://github.com/nf-core/sopa/releases/tag/1.0.0

#segmentation #spatialomics #spatialproteomics #spatialtranscriptomics #spatialdata #nfcore #openscience #nextflow #bioinformatics

Running Until: Iterative Loops in #Nextflow https://seqera.io/blog/running-until-iterative-loops-in-nextflow/

Running Until: Iterative Loops in #Nextflow https://seqera.io/blog/running-until-iterative-loops-in-nextflow/

Pipeline release! nf-core/seqinspector v1.1.0 - nf-core/seqinspector 1.1.0 - Veronica Mars!
Dedicated QC-only pipeline for sequencing data. The pipeline will run a (potentially large) set of QC tools and can output global and group specific Multiqc reports. The pipeline is targeting core facilities or research groups with larger sequencing throughput.
Please see the changelog: https://github.com/nf-core/seqinspector/releases/tag/1.1.0

#genomics #qualitycontrol #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/seqinspector v1.1.0 - nf-core/seqinspector 1.1.0 - Veronica Mars!
Dedicated QC-only pipeline for sequencing data. The pipeline will run a (potentially large) set of QC tools and can output global and group specific Multiqc reports. The pipeline is targeting core facilities or research groups with larger sequencing throughput.
Please see the changelog: https://github.com/nf-core/seqinspector/releases/tag/1.1.0

#genomics #qualitycontrol #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/raredisease v3.1.2 - 3.1.2 - Princess Peach (patch)!
Call and score variants from WGS/WES of rare disease patients.
Please see the changelog: https://github.com/nf-core/raredisease/releases/tag/3.1.2

#diagnostics #raredisease #snv #structuralvariants #variantannotation #variantcalling #wes #wgs #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/raredisease v3.1.2 - 3.1.2 - Princess Peach (patch)!
Call and score variants from WGS/WES of rare disease patients.
Please see the changelog: https://github.com/nf-core/raredisease/releases/tag/3.1.2

#diagnostics #raredisease #snv #structuralvariants #variantannotation #variantcalling #wes #wgs #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/scrnaseq v4.2.0 - 4.2.0!
Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
Please see the changelog: https://github.com/nf-core/scrnaseq/releases/tag/4.2.0

#10xgenomics #10xgenomics #alevin #bustools #cellranger #kallisto #rnaseq #singlecell #starsolo #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/scrnaseq v4.2.0 - 4.2.0!
Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
Please see the changelog: https://github.com/nf-core/scrnaseq/releases/tag/4.2.0

#10xgenomics #10xgenomics #alevin #bustools #cellranger #kallisto #rnaseq #singlecell #starsolo #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/createtaxdb v3.1.0 - v3.1.0 - Seductive Siren - [2026-07-03]!
Parallelised and automated construction of metagenomic classifier databases of different tools
Please see the changelog: https://github.com/nf-core/createtaxdb/releases/tag/3.1.0

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

Pipeline release! nf-core/createtaxdb v3.1.0 - v3.1.0 - Seductive Siren - [2026-07-03]!
Parallelised and automated construction of metagenomic classifier databases of different tools
Please see the changelog: https://github.com/nf-core/createtaxdb/releases/tag/3.1.0

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

Pipeline release! nf-core/mcmicro v2.0.0 - 2.0.0!
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
Please see the changelog: https://github.com/nf-core/mcmicro/releases/tag/2.0.0

#bioformats #imageanalysis #imageprocessing #microscopy #multiplexedimaging #ometiff #registration #segmentation #singlecell #spatial #stitching #tma #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/mcmicro v2.0.0 - 2.0.0!
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
Please see the changelog: https://github.com/nf-core/mcmicro/releases/tag/2.0.0

#bioformats #imageanalysis #imageprocessing #microscopy #multiplexedimaging #ometiff #registration #segmentation #singlecell #spatial #stitching #tma #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/viralmetagenome v1.1.3 - v1.1.3 - Cerulean Crane !
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/1.1.3

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

Pipeline release! nf-core/viralmetagenome v1.1.3 - v1.1.3 - Cerulean Crane !
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/1.1.3

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

Pipeline release! nf-core/mcmicro v2.0.0 - 2.0.0!
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
Please see the changelog: https://github.com/nf-core/mcmicro/releases/tag/2.0.0

#bioformats #imageanalysis #imageprocessing #microscopy #multiplexedimaging #ometiff #registration #segmentation #singlecell #spatial #stitching #tma #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/mcmicro v2.0.0 - 2.0.0!
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
Please see the changelog: https://github.com/nf-core/mcmicro/releases/tag/2.0.0

#bioformats #imageanalysis #imageprocessing #microscopy #multiplexedimaging #ometiff #registration #segmentation #singlecell #spatial #stitching #tma #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/sarek v3.9.0 - 3.9.0 - Sarvesjåhkå!
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/3.9.0

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

Pipeline release! nf-core/sarek v3.9.0 - 3.9.0 - Sarvesjåhkå!
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/3.9.0

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

Pipeline release! nf-core/pairgenomealign v3.0.1 - nf-core/pairgenomealign v3.0.1 – Tokoroten!
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/3.0.1

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

Pipeline release! nf-core/pairgenomealign v3.0.1 - nf-core/pairgenomealign v3.0.1 – Tokoroten!
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/3.0.1

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

Pipeline release! nf-core/rnadnavar v1.0.0 - 1.0.0 - restless hermit!
Pipeline for RNA and DNA integrated analysis for somatic mutation detection
Please see the changelog: https://github.com/nf-core/rnadnavar/releases/tag/1.0.0

#nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/rnadnavar v1.0.0 - 1.0.0 - restless hermit!
Pipeline for RNA and DNA integrated analysis for somatic mutation detection
Please see the changelog: https://github.com/nf-core/rnadnavar/releases/tag/1.0.0

#nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/funcscan v4.0.0 - v4.0.0 - Chinese Baozi - 2026-06-27!
(Meta-)genome screening for functional and natural product gene sequences
Please see the changelog: https://github.com/nf-core/funcscan/releases/tag/4.0.0

#amp #amr #antibioticresistance #antimicrobialpeptides #antimicrobialresistancegenes #arg #assembly #bgc #biosyntheticgeneclusters #contigs #function #metagenomics #naturalproducts #screening #secondarymetabolites #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/funcscan v4.0.0 - v4.0.0 - Chinese Baozi - 2026-06-27!
(Meta-)genome screening for functional and natural product gene sequences
Please see the changelog: https://github.com/nf-core/funcscan/releases/tag/4.0.0

#amp #amr #antibioticresistance #antimicrobialpeptides #antimicrobialresistancegenes #arg #assembly #bgc #biosyntheticgeneclusters #contigs #function #metagenomics #naturalproducts #screening #secondarymetabolites #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/scnanoseq v1.3.0 - nf-core/scnanoseq v1.3.0 - Steel Elephant!
Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.3.0

#10xgenomics #longreadsequencing #nanopore #rnaseq #rnaseq #scrnaseq #singlecell #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/scnanoseq v1.3.0 - nf-core/scnanoseq v1.3.0 - Steel Elephant!
Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.3.0

#10xgenomics #longreadsequencing #nanopore #rnaseq #rnaseq #scrnaseq #singlecell #nfcore #openscience #nextflow #bioinformatics