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chanzuckerberg / czid-web

Infectious Disease Sequencing Platform
https://czid.org/
MIT License
79 stars 24 forks source link

parse_wdl_workflow.py: workarounds for new host filtering WDL #3393

Closed mlin closed 2 years ago

mlin commented 2 years ago

@j-x-han @ovalenzuela19 @morsecodist @rzlim08 here are minimal changes to parse_wdl_workflow.py to make it work on the new host filtering WDL (mainly by just ignoring cases it didn't handle before). Forgive me I can't say I know how the output is used and whether therefore that's the right thing to do -- advice welcome of course....

Invocation:

scripts/parse_wdl_workflow.py < <(curl -sL https://raw.githubusercontent.com/chanzuckerberg/czid-workflows/mlin/modernize-host-filter/short-read-mngs/host_filter.wdl)
mlin commented 2 years ago

@ovalenzuela19 Just bumping this now that we're getting more active

mlin commented 2 years ago

Moved over to https://github.com/chanzuckerberg/czid-web-private/pull/2486