Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Running multiple pipelines with nf-scil on clusters on a lot of subjects #48

Open
AlexVCaron opened this issue Jan 8, 2024 · 1 comment
Labels
bug Something isn't working waiting Waiting for other things to go through

Comments

@AlexVCaron
Copy link
Collaborator

AlexVCaron commented Jan 8, 2024

Running multiple pipelines, or a long sequence of processes, will create a lot of intermediary files. This will not work on clusters, where we already have problems (tractflow+rbx+qc on both for 700 subjects doesn't work).

We'll have to either let go of resume, or use a strategy to lower the number of files and their sizes. This blog post describes a way to reduce file size in the work directory.

Note however that Nextflow is working on this problem right now : nextflow-io/nextflow#3849

@AlexVCaron
Copy link
Collaborator Author

AlexVCaron commented Feb 23, 2024

@AlexVCaron AlexVCaron added the waiting Waiting for other things to go through label Feb 23, 2024
@AlexVCaron AlexVCaron added the bug Something isn't working label Apr 3, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working waiting Waiting for other things to go through
Projects
None yet
Development

No branches or pull requests

1 participant