Adding fix for LD_LIBRARY_PATH in singularity mode

[asp8200]

We had severe problems getting Nextflow to run the Sentieon-images from https://depot.galaxyproject.org/singularity/sentieon%3A202308--h43eeafb_0
in singularity-mode.

Don Freed of Sentieon identified the problem, and Pontus found the fix presented in this PR.

I've tested the fix with Sentieon and I can now run the following test:

nextflow run main.nf -profile test_cache,software_license,<env> --sentieon_extension --aligner sentieon-bwamem --outdir results

with <env> set to docker, singularity and conda.

If the solution is satisfactory, then I'll implement it in the other Sentieon-modules.

PR checklist

Closes #XXX

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  • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

[pontus]

Looks ok.

[maxulysse]

LGTM

[asp8200]

CI-tests failing but I think that is all due to API rate limit exceeded.

[DonFreed]

This seems OK to me.

I would prefer that this is fixed in the container (which seems to require a change in the biocontainers build process). However, I understand that might not be feasible. This seems like an acceptable workaround to get this working quickly.