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Update to the latest simpleaf #312
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Hi @DongzeHE, we are of course happy to support the latest version of simpleaf and would appreciate a PR.
Do you envisage any additional pipeline-level parameters would be needed to support that? Or do you think the Best, |
Hi @grst, Thanks for the reply! For the parameters, I think there are two ways to go:
Tagging @rob-p here in case I missed anything.
It would be great if you could provide some advice on which way we should go, exposing all options or only the most essential ones. Once we figure this out, I am very happy to work on this and submit a PR. Best, |
sounds good. I think we should only expose the most frequently used options on the pipeline level (and those that require an additional input file). Users can still set arbitrary tool options via a config file, e.g. process {
withName: SIMPLEAF {
ext.args = "--no-piscem"
}
} |
Hi @grst , I will create a pull request soon. |
Description of feature
Dear scrnaseq team,
Thank you very much for including simpleaf in
scrnaseq
.Recently, we made major changes to simpleaf, including adding new features and fixing bugs.
simpleaf workflow
module and provided pre-built workflow templates for analyzing data from CITE-seq, 10X feature barcoding, etc.As we noticed that currently, scrnaseq is using an old version of simpleaf, here we want to discuss the possibility of upgrading simpleaf to the latest version, and exposing the new features provided by the latest version.
Tagging @rob-p here in case I missed anything.
Best,
Dongze
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