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SystemsGenetics / GEMmaker

A workflow for construction of Gene Expression count Matrices (GEMs). Useful for Differential Gene Expression (DGE) analysis and Gene Co-Expression Network (GCN) construction
https://gemmaker.readthedocs.io/en/latest/
MIT License
33 stars 16 forks source link

Palmetto fixes #240

Closed bentsherman closed 2 years ago

bentsherman commented 2 years ago

This PR fixes an error we experienced on Palmetto in which retrieve_sra_metadata.py couldn't save meta files to disk. The root cause was that singularity doesn't mount the work/GEMmaker directory by default, so I added a line to nextflow.config that should provide a generic solution.

Additionally, I added the pbs profile back to nextflow.config, as we need it to provide some Palmetto-specific settings. I know a lot of things got moved around during the nf-core upgrade, so if there is a preferred way to provide these extra profiles then I'm happy to adjust it, but I would like this profile to be somewhere in the repo. Otherwise we'll just be passing a random code snippet through various slack channels.

bentsherman commented 2 years ago

I'm not sure what's going on with the nf-core linting and workflow tests, but the errors don't seem to be related to my changes.

bentsherman commented 2 years ago

Closing this PR in favor of a new branch with various tweaks.