refactor parameters - Githubissues

ChristopherBarrington / scamp

single cell analysis and more pipeline

https://christopherbarrington.github.io/scamp/

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refactor parameters #94

Closed ChristopherBarrington closed 11 months ago

ChristopherBarrington commented 11 months ago

the analysis-level stanza makes little sense for most cases.

it could be simplified by using _datasets which would be more consistent with the rest of the parameters file
would mean that _* is not needed
only one _defaults
separate out pipeline runs into directories rather than try to bunch everything in one place
simplifies documentation

[x] parameters script
[x] guessing script
[x] configuration docs
[x] configuration shepherds
[x] user configurable parameters doc
[x] workflow quantification cell ranger arc
[x] workflow quantification cell ranger
[x] seurat prepare cell ranger arc
[x] seurat prepare cell ranger
[x] assets/params
[ ] don't need unique id any more, just use dataset name instead in the workflows?