Meine Pipeline zur Proteinfaltung ist nicht durch gelaufen, weil ich wohl die GPU nicht richtig mit gegeben hab. 
Naja. Morgen halt nochmal starten. 
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Continued thread
Before I continue uploading - and I do have a couple of more contributions to add to the #ResearchEquals collection - first another contribution by Johanna Elena Schmitz and Jens Zentgraf made at the #SnakemakeHackathon2025
One difficulty when dealing with a different scientific question: Do I need to re-invent the wheel (read: write a Workflow from scratch?) just to address my slightly different question?
Snakemake already allowed to incorporate "alien" workflows, even #Nextflow workflows, into desired workflows. The new contribution allows for a more dynamic contribution - with very little changes.
Check it out: https://zenodo.org/records/15489694
ZenodoAllowing Dynamic Load of Modules for SnakemakeSnakemake modules had to be explicitly defined and loaded at the beginning of a workflow. This limited the flexibility of workflows, particularly when dealing with complex dependency structures or when modules needed to be loaded conditionally based on runtime parameters. This contribution eases the procedure of dynamically adding 3rd party modules.
Since we can't use the cloud to automate our #EHR analysis projects , we tried #nextflow (traditionally used in bioinformatics https://www.nextflow.io/), and it worked as a charm coordinating #duckdb #R #python and within node tasks.
Next in line is (R)?ex https://www.rexify.org/
www.nextflow.ioA DSL for parallel and scalable computational pipelines | NextflowNextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.
Since we can't use the cloud to automate our #EHR analysis projects , we tried #nextflow (traditionally used in bioinformatics https://www.nextflow.io/), and it worked as a charm coordinating #duckdb #R #python and within node tasks.
Next in line is (R)?ex https://www.rexify.org/
www.nextflow.ioA DSL for parallel and scalable computational pipelines | NextflowNextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.
Since we can't use the cloud to automate our #EHR analysis projects , we tried #nextflow (traditionally used in bioinformatics https://www.nextflow.io/), and it worked as a charm coordinating #duckdb #R #python and within node tasks.
Next in line is (R)?ex https://www.rexify.org/
www.nextflow.ioA DSL for parallel and scalable computational pipelines | NextflowNextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.
Need help with anything #nfcore #nextflow (#bioinformatics) pipelines, whether running or developing?
Today's EMEA friendly weekly helpdesk is at 10:00-11:00 CEST (Berlin time) on the nf-core gather.town! https://nf-co.re/join#gather-town
Note that we also have other regular helpdesks for different TZs!
- 
Asia-Pacific: Wednesdays @ 15:00 NZDT
- 
Americas: Tuesdays @ 14:00 ET
Join the nf-core slack for more details and reminders!
nf-co.reJoin nf-coreRead about the different ways you can get involved with nf-core
do you want to use #nextflow in #kubernetes but think it's difficult ?
I wrote this post about how to create a "dev environment" using k3d so you can run your pipelines in #k8s easily before to go to prod
comments are welcome
jorge-aguilera.blogExecuting Nextflow pipelines with K3d
https://nf-co.re/docs/contributing/project_proposals
"The nf-core ‘Request for Comment’ (RFC) process is designed to give the community a voice and visibility to large projects that affect the entire community."
nf-co.reDocs: Project proposals / RFCsProcess for proposing major new nf-core projects
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
GitHubRelease 2.2.0 - Kathleen Booth · nf-core/bamtofastqWhat's Changed
Added fastqutils/info to check for truncated or quality-mismatched files by @famosab in #120
Convert the pipeline-level pytest tests to nf-test and use them for CI testing by @maxu...
I put the new `nextflow lint` in my gitlab CI/CD .
> "323 files had 3041 errors" 
https://seqera.io/blog/nextflow-updates-strict-syntax-data-lineage/ "#Nextflow Feature Highlights: Syntax Parser, Native Data Lineage, and Workflow Outputs"
seqera.ioNextflow Feature Highlights: Syntax Parser, Native Data Lineage, and Workflow Outputs | SeqeraAt Nextflow Summit Boston 2025, Seqera CTO and co-founder Paolo Di Tomasso unveiled a series of exciting Nextflow updates as part of the 25.04 release, all designed to enhance clarity, control, and collaboration in workflow development. From stricter syntax and smarter workflow input/output handling to native provenance tracking, this release empowers developers with a more powerful, intuitive, and reproducible experience.
Need help with anything #nfcore #nextflow (#bioinformatics) pipelines, whether running or developing?
Today's EMEA friendly weekly helpdesk is at 10:00 CEST (Berlin time) on the nf-core gather.town! https://nf-co.re/join#gather-town
Note that we also have other regular helpdesks for different TZs!
- Asia-Pacific: Wednesdays @ 15:00 NZDT
- Americas: Tuesdays @ 14:00 ET
Join the nf-core slack for more details and reminders!
nf-co.reJoin nf-coreRead about the different ways you can get involved with nf-core
Do you want to create a plugin and dont know how/where to start?
Are you creating plugins and feel bored repeting again and again the same initial setps?
I just published nf-plugin-generator-cli , a command line tool to create #nextflow plugins:
- name your plugin as you want
- specify your own package
- generate java or groovy version (groovy by the moment)
- asciidoctor documentation
if you want to give a try and give feedback I'll be more than happy
GitHubGitHub - incsteps/nf-plugin-generator-cli: A command line Nexflow plugin generatorA command line Nexflow plugin generator. Contribute to incsteps/nf-plugin-generator-cli development by creating an account on GitHub.
#nextflow DuckdbCache 1.0.0-rc2 released
Nextflow's #DuckDB Cache Plugin enables the storage of task execution metadata in a DuckDB database, ensuring data persistence and scalability. This plugin is particularly useful for workflows that require robust, centralized caching mechanisms across distributed environments.
Read more at
incsteps.github.ionf-duckdbcache: DuckDB cache for Nextflow
Check it out - after almost no design changes in 10 years, the #Nextflow website just got a revamp 
https://www.nextflow.io
Some of the content is still a bit dated / wonky, hoping to address that soon. Would love to hear what folks think!
www.nextflow.ioA DSL for parallel and scalable computational pipelines | NextflowNextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.
Pipeline release! nf-core/rnavar v1.1.0 - nf-core/rnavar 1.1.0 - Mighty Milano!
Please see the changelog: https://github.com/nf-core/rnavar/releases/tag/1.1.0
GitHubRelease nf-core/rnavar 1.1.0 - Mighty Milano · nf-core/rnavar1.1.0 - 2025-04-10
Added
#116 - Added unzip from nf-core modules for working with unzipped fasta and gtf files
#157 - Added support for bam and cram input files
#169 - Added the --star_max_intron_...
Pipeline release! nf-core/mag v3.4.0 - mag 3.4.0 - Green Gecko!
Please see the changelog: https://github.com/nf-core/mag/releases/tag/3.4.0
GitHubRelease mag 3.4.0 - Green Gecko · nf-core/magAdded
#745 - Added pipeline parameter spades_downstreaminput to use contigs instead of scaffolds (by @Pranjal-Bioinfo, @jfy133, @GallVp & @sateeshperi).
#745 - Added trimmomatic as an additional p...
Pipeline release! nf-core/variantbenchmarking v1.2.0 - 1.2.0 Doubtful Adams!
Please see the changelog: https://github.com/nf-core/variantbenchmarking/releases/tag/1.2.0
GitHubRelease 1.2.0 Doubtful Adams · nf-core/variantbenchmarkingWhat's Changed
159 custom bed files by @kubranarci in #167
Json schema improvements by @nvnieuwk in #168
logo cleanup by @kbestak in #171
modify bcftools_reheader to local by @kubranarci in #170
P...