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imgag / megSAP

a Medical Genetics Sequence Analysis Pipeline
GNU General Public License v3.0
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Calls to DB dependent tool when running without db #309

Open BeneKenobi opened 4 days ago

BeneKenobi commented 4 days ago

At https://github.com/imgag/megSAP/blob/a29981c561e27c9b4dc5a60bf95955d129235122/src/Pipelines/analyze.php#L735 and https://github.com/imgag/megSAP/blob/a29981c561e27c9b4dc5a60bf95955d129235122/src/Pipelines/analyze.php#L747

BedAnnotateGenes is called without checking for DB availability which is usually done in other places: https://github.com/imgag/megSAP/blob/a29981c561e27c9b4dc5a60bf95955d129235122/src/Pipelines/analyze.php#L249

marc-sturm commented 4 days ago

CNV calling needs the gene annotations... I guess you would need to skip the whole CNV step if there is no NGSD.

BeneKenobi commented 4 days ago

Is there a possibility to provide the data without a direct connection?