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@jorgee
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@jorgee jorgee commented Nov 6, 2025

This PR includes a draft implemenation of the fs, push and launch command to allow to store git repositories in Seqera platform data-links.

Limitations:

  • Due to the delete limitation with data links, it only works for seqeracompute data-links
  • Nextflow launch fails when submitting the launch because seqera schema is not valid schema for a repo in Seqera platform

For a local test:

$ nextflow push seqera://test-25-g4sikceeu/launch-repos/test -d new-repo-dir
Pushing folder /home/jorgee/nextflow_tests/seqera-git-remote/new-repo-dir to repository seqera://test-25-g4sikceeu/launch-repos/test
WARN: Found 1 large files that would be committed:
WARN:   big_file.data: 15.0 MB
Do you want to push these large files? [y/N]: N
Added 1 large files to .gitignore
Files have been added to .gitignore
Added 2 Nextflow entries to .gitignore: .nextflow, .nextflow.log*

Files to be committed:
  .gitignore
  main.nf
  nextflow.config

Do you want to commit these files? [Y/n]: Y
Successfully pushed to seqera://test-25-g4sikceeu/launch-repos/test (revision: main)

$ nextflow run seqera://test-25-g4sikceeu/launch-repos/test

 N E X T F L O W   ~  version 25.10.0

Pulling test-25-g4sikceeu/launch-repos/test ...
 downloaded from seqera://test-25-g4sikceeu/launch-repos/test
Launching `seqera://test-25-g4sikceeu/launch-repos/test` [zen_brown] DSL2 - revision: 44066a232f [main]

Monitor the execution with Seqera Platform using this URL: https://cloud.seqera.io/orgMonitor the execution with Seqera Platform using this URL: https://cloud.seqera.io/orgMonitor the execution with Seqera Platform using this URL: https://cloud.seqera.io/orgs/seqeralabs/workspaces/testing/watch/1I92X7U7I2bcfZ
executor >  local (4)
[19/89128a] sayHello (1) | 4 of 4 ✔
Hey! Hola world!

Hey! Ciao world!

Hey! Hello world!

Hey! Bonjour world!

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netlify bot commented Nov 6, 2025

Deploy Preview for nextflow-docs-staging canceled.

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🔨 Latest commit 76f401a
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@pditommaso
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pditommaso commented Nov 6, 2025

Not sure we should purse this approach, as a user I'd like to push to any bucket, irrespective of data links

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3 participants