basic filtering steps still using cmo_resources.json

mskcc / roslin-cwl

CWLs for the Roslin Variant Pipeline

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basic filtering steps still using cmo_resources.json #5

Closed allanbolipata closed 5 years ago

allanbolipata commented 5 years ago

See full error log in /juno/work/pi/prototypes/mskcc-cwl/test_runs/cmo_resources.json.err.log

It looks like some imports are still using cmo_resources.json, which is located in /opt/common/CentOS_6-dev/cmo/. I believe it worked before because /opt/common is considered a "singularity bind", but again I'm still not sure we can import these environmental variables and consider roslin-cwl portable.

We will need to figure out a way to remove this dependency.

allanbolipata commented 5 years ago

@nikhil has completed this with https://github.com/mskcc/roslin-cwl/commit/74b34a1718e4871aa8ef63a7d359282fb2c290ec