nf-core
DSL1 > DSL2 migration
A number of "Approved" pipelines in nf-core/pipelines can only run using Nextflow 22.10.x:
Nextflow DSL1 is no longer supported — Update your script to DSL2, or use Nextflow 22.10.x or earlier
These are pipelines run using Nextflow 24.10.5 using the following:
nextflow run nf-core/<pipeline> -r <version> -profile test,docker --outdir test
The "Approved" pipelines (ranked by stars) and versions that fail with this error are:
| Pipeline | Version |
|---|---|
| eager | 2.5.2 |
| proteomicslfq | 1.0.0 |
| imcyto | 1.0.0 |
| clipseq | 1.0.0 |
| dualrnaseq | 1.0.0 |
| kmermaid | 0.1.0-alpha |
| diaproteomics | 1.2.4 |
| mnaseseq | 1.0.0 |
| cageseq | 1.0.2 |
| coproid | 1.1.1 |
| slamseq | 1.0.0 |
| pgdb | 1.0.0 |
coproid is already a separate issue (https://github.com/nf-core/coproid/issues/65), these could (and probably should) be converted to sub-issues?
This page might have saved you some work: https://nf-co.re/pipeline_health
Yep, it really would have. Thanks for that.
Why is this on the modules repo?
I have no idea, it's not something I did. It's either automatic or done by someone else. I simply opened this issue to highlight the pipelines that need migration, and linked relevant issues. Other than that I can't work on it as I have other commitments, so I'm relying on people opening relevant sub-issues and taking it from there.