run nf-test with awsbatch executor

[fmalmeida]

Hy dev team, Thanks for this nice tool.

When trying to execute nf-test with awsbatch it failes with:

Nextflow stderr:

  When using `awsbatch` executor an S3 bucket must be provided as working directory using either the `-bucket-dir` or `-work-dir` command line option

even tough workDir is set to a S3 path in nf-test.config.

I saw that the S3 path actually was created locally by nf-test. So my question are:

• Is this a known limitation by design? If so, there are plans for integration?
• Or else, is there something wrong that nees fine-tuning?

💭

[seppinho]

Yes, that's currently a known limitation. We were discussing this internally today and we see the advantage of having this. We'll come back to you when we have a plan how to integrate that.

[blaurenczy]

Hi! I see that this question here about awsbatch is very much related to mine (here: https://github.com/askimed/nf-test/issues/91) about Azure Cloud, so I understand this feature has been considered but there is no plan yet?

[ivopieniak]

That would be fantastic feature! +1

[blazejszczerba]

Hey, any progress on that ?

[arondaniel]

Hello,

In your nf-test.config you can add: options "-bucket-dir s3://your-bucket/some/path"

This at least allows my test to run with an awsbatch profile. However any files returned in output channels will be at that s3 location.