nf-core / demo

nf-core/demo is a simple nf-core style bioinformatics pipeline for workshops and demos.
https://nf-co.re/demo
MIT License
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gitpod nextflow version too low for demo workflow #20

Open FelixHomma opened 3 weeks ago

FelixHomma commented 3 weeks ago

Description of the bug

Summary

The nextflow version in the gitpod is too low for the demo workflow. I used the Gitpod environment as described in the nf-core/demo tutorial

nf-customize -> nextflow run nf-core/demo -profile test --outdir results
Nextflow 24.09.2-edge is available - Please consider updating your version to it

 N E X T F L O W   ~  version 24.02.0-edge

 ┃ Launching `https://github.com/nf-core/demo` [high_brenner] DSL2 - revision: 04060b4644 [master]

Downloading plugin nf-schema@2.1.1
Nextflow version 24.02.0-edge does not match workflow required version: >=24.04.2

I tried to update nextflow, but to no avail:

nf-customize -> nextflow self-update

      N E X T F L O W
      version 24.09.2-edge build 5927
      created 14-10-2024 21:22 UTC 
      cite doi:10.1038/nbt.3820
      http://nextflow.io

Nextflow installation completed. Please note:
- the executable file `nextflow` has been created in the folder: /opt/conda/bin

nf-customize -> nextflow info
  Version: 24.02.0-edge build 5907
  Created: 10-03-2024 19:56 UTC 
  System: Linux 6.1.91-060191-generic
  Runtime: Groovy 4.0.19 on OpenJDK 64-Bit Server VM 17.0.13-internal+0-adhoc..src
  Encoding: UTF-8 (UTF-8)

Is there another way to update nextflow on gitpod?

Command used and terminal output

nf-customize -> nextflow run nf-core/demo -profile test --outdir results Nextflow 24.09.2-edge is available - Please consider updating your version to it

N E X T F L O W ~ version 24.02.0-edge

┃ Launching https://github.com/nf-core/demo [high_brenner] DSL2 - revision: 04060b4644 [master]

Downloading plugin nf-schema@2.1.1 Nextflow version 24.02.0-edge does not match workflow required version: >=24.04.2 nf-customize -> nextflow self-update

  N E X T F L O W
  version 24.09.2-edge build 5927
  created 14-10-2024 21:22 UTC 
  cite doi:10.1038/nbt.3820
  http://nextflow.io

Nextflow installation completed. Please note:

nf-customize -> nextflow info Version: 24.02.0-edge build 5907 Created: 10-03-2024 19:56 UTC System: Linux 6.1.91-060191-generic Runtime: Groovy 4.0.19 on OpenJDK 64-Bit Server VM 17.0.13-internal+0-adhoc..src Encoding: UTF-8 (UTF-8)

Relevant files

No response

System information

I used the Gitpod environment as described in the nf-core/demo tutorial

christopher-hakkaart commented 3 weeks ago

Thanks @FelixHomma. I found the same thing. I'll get a PR in to reduce.