Experience with setting up S3 buckets wanted: I’ve set up an S3 bucket on a slurm HPC (correctly I believe because it works; can transfer files to it from commandline), however it doesn’t work within a nextflow pipeline (nf-core/funcscan in this case):
First lines in the screenshot show a succeeded pipeline without any S3 path, next lines with S3
--outdir
not working.
Maybe the nf-amazon plugin doesn’t pick up the correct endpoint path? Did you ever see this error?
nextflow config:
process.executor = 'slurm'
docker.enabled = true
aws.client.endpoint = 'https://openstack.cebitec.uni-bielefeld.de:8080/'
aws.client.protocol = 'https'
aws.client.s3PathStyleAccess = true
aws.client.accessKey = 'jasmins_secret_number'
aws.client.secretKey = 'jasmins_secret_number'