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chanzuckerberg / idseq-workflows

Portable WDL workflows for IDseq production pipelines
https://idseq.net/
MIT License
31 stars 12 forks source link

Add optional usegsnapl option #25

Closed morsecodist closed 4 years ago

morsecodist commented 4 years ago

Add optional option to set gsnap vs gsnapl. This allows us to default to gsnap locally and gsnapl remotely but still provides the option for a manual override.

morsecodist commented 4 years ago

Not sure why the test is failing. I don't really understand the error. Does anyone know?

mlin commented 4 years ago

https://github.com/chanzuckerberg/idseq-workflows/pull/26 should fix the test. sorry

mlin commented 4 years ago

@morsecodist when the non_host_alignment.wdl gsnap task is stable to your satisfaction, we'll also want to port the new option to the gsnap task in host_filter.wdl. I'll be glad to help with that