2 remove runcript from singularity build

[munishchouhan]

This PR will remove %runscript from singularity image and make it simple

[pditommaso]

leave to @marcodelapierre to confirm

[pditommaso]

Working in my tests, leave Marco propose any change post-merging

[marcodelapierre]

Changes look good, two important comments, especially the first one:

1. If still as is, I strongly recommend using singularity exec instead of singularity run, as this is the correct, supported usage for Singularity (see singularity docs, https://docs.sylabs.io/guides/latest/user-guide/quick_start.html#executing-commands vs https://docs.sylabs.io/guides/latest/user-guide/quick_start.html#running-a-container

2. The image hash for singularity vs docker is different, right?

[pditommaso]

The image hash for singularity vs docker is different, right?

yes

If still as is, I strongly recommend using singularity exec instead of singularity run

The rationale was to align to the Docker entrypoint behaviour, especially for the problem of Conda initialization. See here. However, I understand that also run can have negative side effects. Let's discussion on nextflow repo

[marcodelapierre]

Hi @pditommaso have a look at this comment of mine:

seqeralabs/wave#288 (comment).

Although I need to have a closer look at the scripts/requirements for mamba-org/micromamba-docker#155 (comment), I am pretty sure that the /.singularity.d/env/ approach would fix singularity exec and singularity shell, including that case.

It looks to me like right now Nextflow is still using exec, right? See https://github.com/nextflow-io/nextflow/blob/master/modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy#L63

So please let me know how you would best like to follow up on this, based on the extra info above.

[pditommaso]

There has been a tentative to use run instead of exec to align it with Docker nextflow-io/nextflow@a1e1d3ca.

However I've reverted this change in the last release nextflow-io/nextflow@c1cc60dd

[marcodelapierre]

Thanks for sharing these code refs Paolo 👍