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Provide google storage object as input to -params-file #5390

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peter-fsdx opened this issue Oct 10, 2024 · 0 comments
Open

Provide google storage object as input to -params-file #5390

peter-fsdx opened this issue Oct 10, 2024 · 0 comments

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@peter-fsdx
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New feature

Same request as this ticket. Would like to be able to pass a google storage path to the -params-file option. Currently this does not seem to work like it does for AWS S3 (#1412)

nextflow test.nf -params-file gs://MYBUCKET/test.json

 N E X T F L O W   ~  version 24.04.4

ERROR ~ Cannot initialize GsPathFactory: missing session

 -- Check '.nextflow.log' file for details
ERROR conda.cli.main_run:execute(124): `conda run nextflow test.nf -params-file gs://MYBUCKET/test.json` failed. (See above for error)

Usage scenario

Running nextflow in a cloud environment want to be able to pass the parameters to the pipeline without having a script to copy the file from cloud storage to the VM's disk.

Suggest implementation

Similar to what appears to be the S3 implementation, nextflow already is able to read files from google storage elsewhere in the code. Java/Groovy is not my strong suit but it appears that nextflow is trying to read the params file before the global session is set. Failing here

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