Add support for custom custom root directory to resolve relative paths #3942
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Signed-off-by: Paolo Di Tommaso <[email protected]>
Signed-off-by: Paolo Di Tommaso <[email protected]>
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Solves #2661 |
![sonatype-lift[bot]](https://avatars.githubusercontent.com/in/9843?s=60&v=4){kind=small}
Signed-off-by: Paolo Di Tommaso <[email protected]>
Signed-off-by: Paolo Di Tommaso <[email protected]>
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Look @drpatelh! is happening! 😆 |
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abhi18av
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Oct 28, 2023
nextflow-io#3942) this PR introduces the environment variable `NXF_FILE_ROOT` which can be used to define the root path against which relative paths need to be resolved. For example, having defined the following variable `NXF_FILE_ROOT=s3://my-bucket/data`, the use of `file('foo.txt')` will result in the path `s3://my-bucket/data/foo.txt/` This behaviour applies to file path resolved via the Nextflow built-in functions `file`, `files`, `channel.fromPath`, `channel.fromFilePairs` and the `publishDir` operator.
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Nextflow resolves relative paths against the current working directory following the usual Linux and Java conventions.
For example, if the workflow is execution is launched in the path
/home/yo/workflowand the workflow reference a filefoo.txtusing the functionfile('foo.txt'), the resulting file path will be/home/yo/workflow/foo.txt.This makes sense when working in a local or share file system, howeber it results into counter-intuitive behaviour when using a cloud-containerised execution environment.
In this scenario, Nextflow runs into a container ephemeral file system and relative paths are resolved as local container files that are lost after the job completion.
To solve this problem, this PR introduces the environment variable
NXF_FILE_ROOTthat can be used to define the root path against which relative path needs to be resolved.For example having define the following variable
NXF_FILE_ROOT=s3://my-bucket/data, the use offile('foo.txt')will result in the paths3://my-bucket/data/foo.txt/This behaviour applies to file path resolved via the Nextflow built-in functions
file,files,channel.fromPath,channel.fromFilePairsand thepublishDiroperator.