Using nextflow inspect with Singularity

[ewels]

The new nextflow inspect command is working nicely with Docker, but there is some odd behaviour for singularity.

Requires wave, but shouldn't need to

$ nextflow inspect -r 2.6.0 nf-core/viralrecon -profile singularity,test --outdir .
Inspect command with Singularity requires enabling 'wave' and 'freeze' settings

We don't need to build the Singularity container here, it's already hardcoded in the script. We just want the URI. Is there any way that we can get to it? Source here.

    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
        'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"

Crashes if wave installed but no singularity

When I try locally, I get a different error - probably related:

$ nextflow inspect -r 2.6.0 nf-core/viralrecon -profile singularity,test --outdir .
ERROR ~ java.lang.IllegalStateException: Failed to pull singularity image
  command: singularity pull  --name depot.galaxyproject.org-singularity-ubuntu-20.04.img.pulling.1697732463429 https://depot.galaxyproject.org/singularity/ubuntu:20.04 > /dev/null
  status : 127
  message:
    bash: singularity: command not found

Here it's not trying to use Wave, but it is trying to do singularity pull on the image, when I'm only asking to return the URI.

[pditommaso]

Update to nextflow 23.10.0 !

[pvanheus]

This behaviour (the first example: Inspect command with Singularity requires enabling 'wave' and 'freeze' settings) was seen with nextflow 23.10.0.5889.

So the message comes from here which is called here - the comment there says // disallow singularity w/o wave and freeze so the message lines up with that comment.

[ewels]

Yup, my outputs above are all from 23.10.0

[muffato]

Hiya. I'm seeing the same problem with Nextflow 23.10.0-5889

I was following #4069 and I'm pretty sure I tested it at some point and it was working with Singularity. So maybe a regression from when the integration with Wave was added ?

[pditommaso]

Ok, it is solved! f5bb829