Support Singularity, Output Nextflow Reports to params.outdir - #1
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jeffquinn-msk
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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' |
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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.
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