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secondary files not loaded when in batch runs


I have a tool which analyzes .bam files and requires .bai files as secondary files.
The secondary files settings are ok as the tool works well when a run on a single file is performed.
However, when i try to make a batch task, it doesn't work and the error log says "unable to find index file for example.bam" or something like this.

Is it a known bug? is there a way to overcome this problem?

Thanks a lot!