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wustl-oncology / analysis-wdls

Scalable genomic analysis pipelines, written in WDL
MIT License
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A typo in somatic_exome_nonhuman results in the VCF tumor column being renamed to use the normal sample name #155

Open malachig opened 1 week ago

malachig commented 1 week ago

This appears to be a typo that occurred from CWL to WDL transition, or perhaps existed since the creation of the non-human detect variants pipeline:

Relevant lines in detect_variants_nonhuman.wdl https://github.com/wustl-oncology/analysis-wdls/blob/926e1f9496c04a80baa5892b75ad7d43c617118a/definitions/detect_variants_nonhuman.wdl#L95-L96

Relevant lines in detect_variants.wdl https://github.com/wustl-oncology/analysis-wdls/blob/926e1f9496c04a80baa5892b75ad7d43c617118a/definitions/detect_variants.wdl#L110-L111

malachig commented 1 week ago

Just for provenance sake, this error was NOT present in the CWL version:

https://github.com/genome/analysis-workflows/blob/5fda2d9eb52a363bd51011b3851c2afb86318c0c/definitions/pipelines/detect_variants_nonhuman.cwl#L192-L193