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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

Replace baseDir with projectDir #246

Closed bentsherman closed 2 years ago

bentsherman commented 2 years ago

This PR simply replaces baseDir with projectDir. Both are implicit variables that point to the pipeline directory, mainly used to refer to assests in the GEMmaker repo. However, baseDir does not work with kubernetes and it is also deprecated as of nextflow 20.04.

bentsherman commented 2 years ago

Actually it looks like projectDir doesn't work with kubernetes either. So this PR is just removing a deprecated feature and can be merged whenever.

spficklin commented 2 years ago

Easy fix! Thanks Ben.