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seqeralabs / tower-agent

Agent app that allows connecting remote batch schedulers to Tower Cloud
https://cloud.tower.nf
Apache License 2.0
8 stars 4 forks source link

Tower agent not fetching correct files via github API #43

Closed sandsebi closed 2 years ago

sandsebi commented 2 years ago

I'm trying to run the following pipeline on Tower:

nextflow run https://github.com/enasequence/covid-sequence-analysis-workflow
         -name test-V2
         -with-tower
         -r v2-api-migration
         -main-script nanopore/nanopore.nf

But it errors out with the following:

WARN: Cannot read project manifest -- Cause: Remote resource not found: https://api.github.com/repos/enasequence/covid-sequence-analysis-workflow/contents/nextflow.config
Remote resource not found: https://api.github.com/repos/enasequence/covid-sequence-analysis-workflow/contents/main.nf

Ideally as I've specified the Revision number which in my case is the branch name, the Github API URL's should look like: https://api.github.com/repos/enasequence/covid-sequence-analysis-workflow/contents/nextflow.config?ref=v2-api-migration and https://api.github.com/repos/enasequence/covid-sequence-analysis-workflow/contents/main.nf?ref=v2-api-migration right?

I'm using Tower agent on LSF. Nextflow module version: nextflow-21.10.6-gcc-9.3.0-tkuemwd

pditommaso commented 2 years ago

The problem is that the repository does not have either the nextflow.config or main.nf file in the project root

sandsebi commented 2 years ago

It does have both on the branch v2-api-migration

pditommaso commented 2 years ago

Unfortunely it's not enough. There must be at least the nextflow.config file (even empty) in the default branch

sandsebi commented 2 years ago

Ok thanks 👍 Would have been helpful to document clearly, the need for having a main.nf and a nextflow.config file at the root of the repo.