docs: Managing Nextflow work directory growth#3644
Merged
christopher-hakkaart merged 12 commits intomainfrom Nov 12, 2025
Merged
docs: Managing Nextflow work directory growth#3644christopher-hakkaart merged 12 commits intomainfrom
christopher-hakkaart merged 12 commits intomainfrom
Conversation
✅ Deploy Preview for nf-core-docs ready!
To edit notification comments on pull requests, go to your Netlify project configuration. |
✅ Deploy Preview for nf-core-main-site ready!
To edit notification comments on pull requests, go to your Netlify project configuration. |
Member
Author
|
@nf-core-bot fix linting |
mashehu
reviewed
Nov 11, 2025
sites/docs/src/content/docs/tutorials/storage_utilization/managing_work_directory_growth.md
Outdated
Show resolved
Hide resolved
…ging_work_directory_growth.md Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
ewels
reviewed
Nov 11, 2025
sites/docs/src/content/docs/tutorials/storage_utilization/managing_work_directory_growth.md
Outdated
Show resolved
Hide resolved
ewels
reviewed
Nov 11, 2025
sites/docs/src/content/docs/tutorials/storage_utilization/managing_work_directory_growth.md
Outdated
Show resolved
Hide resolved
sites/docs/src/content/docs/tutorials/storage_utilization/managing_work_directory_growth.md
Outdated
Show resolved
Hide resolved
sites/docs/src/content/docs/tutorials/storage_utilization/managing_work_directory_growth.md
Show resolved
Hide resolved
sites/docs/src/content/docs/tutorials/storage_utilization/managing_work_directory_growth.md
Outdated
Show resolved
Hide resolved
sites/docs/src/content/docs/tutorials/storage_utilization/managing_work_directory_growth.md
Outdated
Show resolved
Hide resolved
sites/docs/src/content/docs/tutorials/storage_utilization/managing_work_directory_growth.md
Outdated
Show resolved
Hide resolved
sites/docs/src/content/docs/tutorials/storage_utilization/managing_work_directory_growth.md
Outdated
Show resolved
Hide resolved
sites/docs/src/content/docs/tutorials/storage_utilization/managing_work_directory_growth.md
Outdated
Show resolved
Hide resolved
sites/docs/src/content/docs/tutorials/storage_utilization/managing_work_directory_growth.md
Outdated
Show resolved
Hide resolved
Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
Member
mahesh-panchal
left a comment
mahesh-panchal
left a comment
There was a problem hiding this comment.
Also in the optimized process, I would recommend adding rm of intermediate files if temp files are used.
sites/docs/src/content/docs/tutorials/storage_utilization/managing_work_directory_growth.md
Outdated
Show resolved
Hide resolved
sites/docs/src/content/docs/tutorials/storage_utilization/managing_work_directory_growth.md
Outdated
Show resolved
Hide resolved
sites/docs/src/content/docs/tutorials/storage_utilization/managing_work_directory_growth.md
Outdated
Show resolved
Hide resolved
sites/docs/src/content/docs/tutorials/storage_utilization/managing_work_directory_growth.md
Show resolved
Hide resolved
Member
Author
|
Thanks for the reviews @mahesh-panchal and @ewels Let me know if there is anything else that can be improved (and that I've captured your comments correctly) |
mahesh-panchal
approved these changes
Nov 12, 2025
sites/docs/src/content/docs/tutorials/storage_utilization/managing_work_directory_growth.md
Outdated
Show resolved
Hide resolved
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
| Nextflow's built-in `clean` command enables targeted removal of work directories. The following command preserves work directories from the current execution while removing directories from previous executions: | ||
|
|
||
| ```bash | ||
| nextflow clean -f -before $(nextflow log -q | tail -n 1) |
Member
There was a problem hiding this comment.
I just learned there's a last keyword so one doesn't need $(nextflow log -q | tail -n 1)
It's barely documented. https://www.nextflow.io/docs/latest/cli.html#execution-logs
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
5 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
@netlify /docs/tutorials/storage_utilization/managing_work_directory_growth