moved the set -o lines under the ACCESS_TOKEN block

wustl-oncology / analysis-wdls

Scalable genomic analysis pipelines, written in WDL

MIT License

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moved the set -o lines under the ACCESS_TOKEN block #133

Closed evelyn-schmidt closed 10 months ago

evelyn-schmidt commented 11 months ago

Attempting to run immuno on compute1 results in varscan failing. @tmooney suggested moving the set -o lines after the wget block. As of now, since errext and pipefail are set before wget, when the command is executed wget does not find the server and it causes a non-zero exit. I have tested this change and it appears that this fix allows varscan to execute successfully.

malachig commented 10 months ago

Performed a test on a full dataset and confirmed that the varscan results are identical (except for expected differences including file paths and time stamps).