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nextflow-io / rnaseq-nf

A proof of concept of RNAseq pipeline
Apache License 2.0
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Error when running GCP tutorial #6

Closed DenisSch closed 3 years ago

DenisSch commented 3 years ago

I am running the GCP tutorial: https://cloud.google.com/life-sciences/docs/tutorials/nextflow

When executing ./nextflow run rnaseq-nf/main.nf -profile gls

I receive the following error:


N E X T F L O W  ~  version 20.10.0
Launching `rnaseq-nf/main.nf` [hopeful_mccarthy] - revision: 29dd20fd3f
Cannot a find a file system provider for scheme: gs
pditommaso commented 3 years ago

What about this ?

NXF_MODE=google ./nextflow run rnaseq-nf/main.nf -profile gls
DenisSch commented 3 years ago

That worked - thank you!

DenisSch commented 3 years ago

Unfortunately, the next error message is: Missing Google credentials -- make sure your environment defines the GOOGLE_APPLICATION_CREDENTIALS environment variable

I have performed the steps in the tutorial - it seems like something is still missing

DenisSch commented 3 years ago

Update: The path needs to be defined directly without {PWD}