Calls to DB dependent tool when running without db

[BeneKenobi]

At

megSAP/src/Pipelines/analyze.php

Line 735 in a29981c

["{$ngsbits}BedAnnotateGenes", "-out {$bed}"]

and

megSAP/src/Pipelines/analyze.php

Line 747 in a29981c

["{$ngsbits}BedAnnotateGenes", "-out {$bed}"],

BedAnnotateGenes is called without checking for DB availability which is usually done in other places:

megSAP/src/Pipelines/analyze.php

Line 249 in a29981c

if (db_is_enabled("NGSD"))

[marc-sturm]

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

[BeneKenobi]

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