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iRNA-COSI / APAeval

Community effort to evaluate computational methods for the detection and quantification of poly(A) sites and estimating their differential usage across RNA-seq samples
MIT License
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docs: Update readme to include mandatory parameters for execution workflow #189

Closed faricazjj closed 2 years ago

faricazjj commented 3 years ago

Each execution workflow should have parameters on which benchmark to run in the config file. The parameters are: run_identification = True/False run_quantification = True/False run_differential = True/False

Only parameters for benchmarks that the workflow qualifies for should be included. For example, if a workflow only qualifies for identification and differential, it should only include: run_identification = True/False run_differential = True/False

This allows for the workflow to output any combination of benchmarks that it qualifies for, as specified by the user.

Readmes to be updated: Execution workflow readme Nextflow template readme Execution workflow dsl1 template readme Execution workflow dsl2 template readme

faricazjj commented 3 years ago

@ninsch3000 @dominikburri @SamBryce-Smith @yuukiiwa @grexor @uniqueg Does this description sound like what we want to go ahead with following up from our meeting today?

ninsch3000 commented 3 years ago

Thanks a lot @faricazjj .
I think it could be useful to also mention that the ewfs might have to run a tool twice under the hood, or any other considerations for coding you have come across (You know better than me since you already wrote so many ewfs!!). I mean, just to give the reader some idea on what they might have to face. And as for "Readmes to be updated": Snakemake template should also be updated :)