when running picard MarkDuplicates the optical_duplicate_pixel_distance parameter is capped at 500, but for patterned flow cells 2500 is optimal (this is even mentioned in the description). Request to edit picard_MarkDuplicates.xml in the tool like so:
"
param name=“optical_duplicate_pixel_distance” type=“integer” value=“100” min=“0” max=“2500” label=“The maximum offset between two duplicte clu
sters in order to consider them optical duplicates” help=“OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100”
"
Hi @odhardy
If you are using the tool at your own server, all of our software is open source. This means you can modify your local copy any way you want.
If you want the primary wrapper adjusted instead (and have it available at public sites), we welcome community contributions. Review will happen during that process (logic, resource considerations, etc.).
- Tool Development contacts Galaxy Working Groups and Projects - Galaxy Community Hub → Tools
- Development repository for this tool https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard