In some processes, extra java arguments and extra command arguments both point on the same configuration variable ext.args - Githubissues

Ferlab-Ste-Justine / Post-processing-Pipeline

Variant analysis for genome and exome VGCFs

Apache License 2.0

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In some processes, extra java arguments and extra command arguments both point on the same configuration variable ext.args #14

Open LysianeBouchard opened 2 months ago

LysianeBouchard commented 2 months ago

Description of the bug

Consequence is that, if I specify a value for ext.args for those processes, it will appear both in java arguments and main executable arguments.

Processes with this behaviour at the moment moment of writing this doc:

importGVCF
hardFiltering
variantRecalibratorSNP
variantRecalibratorIndel
applyVQSRSNP
applyVQSRIndel

It might be a good idea to visit each local process one by one to double check.

Command used and terminal output

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Relevant files

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System information

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