Support Singularity, Output Nextflow Reports to params.outdir
#1
Conversation
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
jeffquinn-msk
commented
Jul 26, 2024
| if (executor == 'docker') { | ||
| return '-u root:root -e USERID=$UID -e XDG_CACHE_HOME=tmp/quarto_cache_home -e XDG_DATA_HOME=tmp/quarto_data_home -e QUARTO_PRINT_STACK=true' | ||
| } else if (executor == 'singularity') { | ||
| return '--env USERID=$UID --env XDG_CACHE_HOME=tmp/quarto_cache_home --env XDG_DATA_HOME=tmp/quarto_data_home --env QUARTO_PRINT_STACK=true' |
Author
There was a problem hiding this comment.
For environment variables it would probably be better to set them in the task definition itself on second thought, passing them to the container options is confusing. Nextflow by default passes all env variables from the calling process down into the container anyway, and for the hardcoded ones, you can hard code them in the process block.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
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Outdated suggestions cannot be applied.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.
No description provided.