Migrate from subprocess to workflow language - Githubissues

cytomining / profiling-recipe

Image-based Profiling Recipe

BSD 3-Clause "New" or "Revised" License

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Migrate from subprocess to workflow language #12

Open gwaybio opened 3 years ago

gwaybio commented 3 years ago

Explore moving from a subprocess-based pipeline step execution strategy to a workflow language.

Some examples include:

wdl - https://github.com/openwdl/wdl
snakemake - https://snakemake.github.io/

How we will make this decision:

We will outline our needs for the immediate and future pipeline (some needs discussed in #11 )
We will determine which option best serves our needs and is most compatible with our tech stack
We will carve out sufficient, dedicated time to make an informed decision

gwaybio commented 2 years ago

noting here that we're developing a snakemake workflow in https://github.com/WayScience/CytoPipe