Gary Burnett
Gary Burnett
Thank you for the extra information! I will talk to the wider team about other solutions.
@famosab I did some more looking into this and it seems like you're getting this error because my original solution involved creating a symlink in the index folder, which you...
I have made some edits to the [PR](https://github.com/nf-core/modules/pull/9308). It removes the requirement for a reference file when writing BAMs (by creating a dummy reference file in the correct location so...
This problem is not unique to Parabricks, but the standard imposed by BWA that Parabricks is following. Even when you're running BWA you need to provide an index and a...
The way bwa uses these flags is not safe. You can pass a reference file to bwa that doesn't exist and it will run anyways, provided it doesn't end up...
Update: We will look into it more. Parabricks updates come once every 6 months so it will be some time before a nore permanent fix can be implemented. For now...
bwa doesn't need to put the fasta in the index folder. It just points to a path in that folder (whether that path exists or not) and then just takes...
@famosab @FriederikeHanssen I made some updates to clean up this PR (filling out the PR checklist and adding better handle the cleanup of the dummy files). Do you support this...