CDCgov / phoenix

🔥🐦🔥PHoeNIx: A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens

https://www.cdc.gov/ncezid/divisions-offices/about-dhqp.html

Apache License 2.0

60 stars 18 forks source link

Update ICA, Terra handling to remove launchdir from module #149

Closed slsevilla closed 5 months ago

slsevilla commented 8 months ago

Description

Currently the ICA handling of scripts is written as variables with the launchDir being called directly in the module. This is affecting the ability for the output of these modules to cache correctly (relating to #129).

Also adding Terra to this type of refactoring

Solution

Rewrite module as a def
Create param for path so that launchDir is only called in the config

jvhagey commented 5 months ago

addressed with https://github.com/CDCgov/phoenix/commit/a17b58fe9d750d42c06afbaa34bdf4c6a1a9ac7f will be in v2.2.0 when its released.