Singularity options at the Crick

[ChristopherBarrington]

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name: Modification to existing Crick config

Please follow these steps before submitting your PR:

• If your PR is a work in progress, include [WIP] in its title
• Your PR targets the master branch
• You've included links to relevant issues, if any

Steps for adding a new config profile:

• Add your custom config file to the conf/ directory
• Add your documentation file to the docs/ directory
• Add your custom profile to the nfcore_custom.config file in the top-level directory
• Add your custom profile to the README.md file in the top-level directory
• Add your profile name to the profile: scope in .github/workflows/main.yml

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Some paths may not be accessible when using Singularity. Adding /nemo and /flask explicitly to runOptions allows paths to files to be correctly resolved. autoMounts is already enabled so I'm not sure why these paths are not exposed.

[maxulysse]

LGTM

[chris-cheshire]

Hi Chris, could you describe what this fixes, or enhances?

[ChristopherBarrington]

We have had problems with singularity not being able to access certain files when using the scratch space (/flask). This wasn't a problem before because scratch was under /camp which was reliably mounted.