Skip to content

Revert the stream swap after the redirect to .command.out and .command.err#7300

Open
tcezard wants to merge 2 commits into
nextflow-io:masterfrom
tcezard:fix/stderr_stdout_swap
Open

Revert the stream swap after the redirect to .command.out and .command.err#7300
tcezard wants to merge 2 commits into
nextflow-io:masterfrom
tcezard:fix/stderr_stdout_swap

Conversation

@tcezard

@tcezard tcezard commented Jul 3, 2026

Copy link
Copy Markdown

fixes #7299
This PR attenpt to fix the stream swap when executing .command.sh in .command.run
It does not change the similar stream swap in nxf_unstage but that might be needed as well.

@netlify

netlify Bot commented Jul 3, 2026

Copy link
Copy Markdown

Deploy Preview for nextflow-docs ready!

Name Link
🔨 Latest commit 572280c
🔍 Latest deploy log https://app.netlify.com/projects/nextflow-docs/deploys/6a58b45345cce50008de6a69
😎 Deploy Preview https://deploy-preview-7300--nextflow-docs.netlify.app
📱 Preview on mobile
Toggle QR Code...

QR Code

Use your smartphone camera to open QR code link.

To edit notification comments on pull requests, go to your Netlify project configuration.

@tcezard
tcezard force-pushed the fix/stderr_stdout_swap branch from ef7d60f to bf71b71 Compare July 3, 2026 12:59
…d.err

---------

Signed-off-by: tcezard <tcezard@ebi.ac.uk>
local start_millis=$(nxf_date)
trap 'kill $mem_proc' ERR

Copy link
Copy Markdown
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This change is unnecessary, and it will break a test

Copy link
Copy Markdown
Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Added the spaces back

Signed-off-by: Timothee Cezard <tcezard@ebi.ac.uk>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Projects

None yet

Development

Successfully merging this pull request may close these issues.

stdout and stderr are swapped by .command.run in SLURM

3 participants