Singularity can't find container

[sara77777777]

Hello,
I made a pipeline in which winnowmap is the first process, but when I run the pipeline.nf I get the error:
winnowmap: command not found
I belive the problem is that singularity can't find the containers.

This is part of my nextflow.config file:

singularity {
        autoMounts = true
        runOptions = "--bind ${params.bind_path}"
}

process {
        errorStrategy = "ignore"
        withName:MAP { container = "winnowmap:2.03--h43eeafb_2" }      
}


dag { enabled = true }
report { enabled = true }
timeline { enabled = true }
trace { enabled = true }

running echo $SINGULARITY_CACHEDIR it returns the path to the directory where I have the image: /work/my_singularity_container.

This is my image:
/work/my_singularity_container/winnowmap-2.03--h43eeafb_2.img.
I downloaded from here:
https://depot.galaxyproject.org/singularity

Can someone help me?

[bentsherman]

You also need to set singularity.enabled = true in your config or use the -with-singularity CLI option

[sara77777777]

I tried using the -with-singularity option but it didn't work, now I'm setting singularity.enabled = true in my config and it's working, so thank you for your help

[colindaven]

I specify the image directly as well, since I use an NFS storage on a cluster

process.container = '/mnt/somepath/image.sif'

[bentsherman]

That's a good point. Until recently, containerized runs would fail if you didn't specify a default container with process.container. This was fixed in the latest edge release, so you shouldn't need to do that anymore as long as you specify it for each process.