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wustl-oncology / analysis-wdls

Scalable genomic analysis pipelines, written in WDL
MIT License
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use pipe instead of redirection for varscan #111

Closed malachig closed 1 year ago

malachig commented 1 year ago

Even if we do set -o pipefail as proposed here, a failed read when streaming directly from a google bucket is not caught when the varscan command is using redirection.

For that reason, this pull request also changes the VarScan command to use a pipe instead.

malachig commented 1 year ago

I tested this manually/locally in the same docker image but will now run a full test run with the mcdb014 data.

malachig commented 1 year ago

This is related to issue: https://github.com/wustl-oncology/analysis-wdls/issues/109

malachig commented 1 year ago

This seems to be working fine with full data tests.