After BAM filtering, the header can be removed. This sounds like your problem. BAMs with no header cause problems with the newer BAM dataset format requirements (are now stricter). We will be updating the tools (details: https://github.com/galaxyproject/usegalaxy-playbook/issues/102).
Which filter tool are you specifically using and which tool produced the input? Was that input SAM or BAM to start with? Please include tool version's and the server where you are working, so we can make sure that is on our list for updates/testing. Or you can send a history share link to firstname.lastname@example.org and note the dataset number and we can capture that info.
To fix that problem:
You'll need to add back in the header and convert to BAM if working with SAM input. This process should now automatically coordinate sort the BAM, but check and coordinate sort after if needed. Then the datatype will be correct (just
bam) and you can adjust any other metadata you need (database, etc). Tools for these tasks are in a few tool groups, in a few versions with different functions, so you can "tool search" those or just review the available tools in SAMTools or Picard first.
If that is not your problem, then definitely do send in a history share link with the same info and we can help troubleshoot if you working at Galaxy Main or can reproduce the problem here: https://usegalaxy.org. If not working at Main or cannot reproduce the problem there, you might need to reach out to your local admins, unless the details can be explained or shared publically with enough detail to reproduce the problem.
- Reporting Usage Issues or Software bugs https://galaxyproject.org/issues/
Thanks! Jen, Galaxy team