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

Call containerOptionsCreator #691

Merged

Conversation

mahesh-panchal
Copy link
Member

Fix to call the containerOptionsCreator rather than assign the closure

@mahesh-panchal mahesh-panchal requested a review from pontus as a code owner May 22, 2024 13:38
@mahesh-panchal mahesh-panchal merged commit 8eeb9eb into nf-core:master May 22, 2024
126 checks passed
@mahesh-panchal mahesh-panchal deleted the patch_unresolved_closure branch May 22, 2024 14:07
@pontus
Copy link
Contributor

pontus commented May 22, 2024

I don't mind this change but out of curiosity; did you have issues related to it? I don't see now why it would cause problems.

@mahesh-panchal
Copy link
Member Author

Nextflow wasn't evaluating the closure. Agata reported it to me. Her run scripts looked like:

	nxf_launch() {
	    set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} SINGULARITYENV_NXF_DEBUG="${NXF_DEBUG:=0}" singularity exec --no-home --pid -B /cfs/klemming/projects Script8C84027CBF0BFB90846176A9D9C58EDE$_run_closure2@3a53a874 /cfs/klemming/projects/snic/--redacted--/containers/depot.galaxyproject.org-singularity-ubuntu-20.04.img /bin/bash -c "cd $PWD; eval $(nxf_container_env); /bin/bash /cfs/klemming/projects/supr/--redacted--/work/df/5238938689a64af1a2c9f34443b5a6/.command.run nxf_trace"
	}

and then nextflow complained it couldn't find the image Script8C84027CBF0BFB90846176A9D9C58EDE$_run_closure2@3a53a874

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants