Confirm that use of BLAST's `-max_target_seqs` is intentional

armish commented 6 years ago

Hi there,

This is a semi-automated message from a fellow bioinformatician. Through a GitHub search, I found that the following source files make use of BLAST's -max_target_seqs parameter:

metapy_tools/shell_scripts/Interogate_controls_all_folders.sh

Based on the recently published report, Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows, there is a strong chance that this parameter is misused in your repository.

If the use of this parameter was intentional, please feel free to ignore and close this issue but I would highly recommend to add a comment to your source code to notify others about this use case. If this is a duplicate issue, please accept my apologies for the redundancy as this simple automation is not smart enough to identify such issues.

Thank you! -- Arman (armish/blast-patrol)

peterthorpe5 commented 6 years ago

This one is a BLASTn example and is misued.

cheers,

Pete

armish commented 6 years ago

OOC: Any plans for fixing or marking it in the code?

peterthorpe5 / public_scripts

Confirm that use of BLAST's `-max_target_seqs` is intentional #7