Weekly Recap (Aug 2025, part 2): Metagenome assembly from nanopore reads, AI for single-cell analysis, GxE + epistasis in a vertebrate model, estimating GxE for polygenic traits, long-read alignment, agents, nf-core, ... doi.org/10.59350/004... #Rstats #nextflow

Using #nextflow to download 1000's of mp3 from youtube

If I understand it correctly you have to pay for what should be considered basic security features in the #nextflow Seqera platform… which is a bit disappointing…

I cannot believe how bad the #copilot suggestions in #vscode are. Anyone got a good IDE for #nextflow?

Massive engineering changes for modularity, #NextFlow workflows, data:code separation, etc - Matthias Blum “InterProScan 6: a modern large-scale protein function annotation pipeline” #BOSC2025 #ISMBECCB2025

You get socks, and you get socks!

Thanks to #BOSC2025 sponsor Seqera #NextFlow for the conference swag

https://seqera.io/

how to use #nextflow "multiMap' to transform a channel if the 'input' of an existing module doesn't fit your needs.

eg: you want

tuple val(meta), path(bam),path(bed)

while the module was designed the following way:

tuple val(meta1), path(bed)
tuple val(meta2), path(bam)

https://gist.github.com/lindenb/fbd76e5887754a7831d95422ea58f499

thanks a lot @mbp for the tip !

{targets} getting a shoutout in @kgagalova’s talk, even though the focus is on #nextflow #RStats #ReproducibleResearch #Bioinformatics #targets. #Pipelines

Pipeline release! nf-core/methylseq v4.0.0 - Wallace Chrysalis!

Please see the changelog: https://github.com/nf-core/methylseq/releases/tag/4.0.0

Fast and Accurate Enrichment of Canid Excrement for Specie* and Other Analyses (FAECES*) Method for Noninvasive Genotyping of Field-Collected Canid Scat pubmed.ncbi.nlm.nih.gov/40580297/ #nextflow

Pipeline release! nf-core/demo v1.0.2 - nf-core/demo 1.0.2 - Mostly Harmless!

Please see the changelog: https://github.com/nf-core/demo/releases/tag/1.0.2

Pipeline release! nf-core/pathogensurveillance v1.0.0 - 1.0.0!

Please see the changelog: https://github.com/nf-core/pathogensurveillance/releases/tag/1.0.0

1/ Ok, so I finally figured out the interesting (i.e. painful) error I’ve been chasing in my #Nextflow genomic mapping pipeline the past few days.
Basically, I’ve got hundreds of bwa mem mapping jobs running as separate processes in Docker containers, grouped on large AWS EC2 instances. Seemingly randomly some samples would fail during the subsequent mark duplicates process due to issues with the read group (@RG) headers.
#bioinformatics #genomics

Pipeline release! nf-core/raredisease v2.6.0 - 2.6.0 - Cacofonix!

Please see the changelog: https://github.com/nf-core/raredisease/releases/tag/2.6.0

I've refactor the #nextflow plugins stats site and now it's under IncSteps domain.

It has not only a new look&feel but also ... you can comment on it (using github discussion integration)!!!!

https://incsteps.github.io/nf-plugins-stats/)

Pipeline release! nf-core/createtaxdb v1.0.0 - v1.0 - Helpful Hydra - [2025-06-19]!

Please see the changelog: https://github.com/nf-core/createtaxdb/releases/tag/1.0.0

Pipeline release! nf-core/metatdenovo v1.2.0 - nf-core/metatdenovo 1.2.0!

Please see the changelog: https://github.com/nf-core/metatdenovo/releases/tag/1.2.0

Pipeline release! nf-core/bamtofastq v2.2.0 - 2.2.0 - Kathleen Booth!

Please see the changelog: https://github.com/nf-core/bamtofastq/releases/tag/2.2.0