Hi there, I'm currently developing a pipeline for chimeric reads detection. Trying to implement yacrd, I stumbled across an issue with minimap2: I need to map the reads back onto themselves. If I do this:

MINIMAP2_ALIGN(reads, reads, [], [], [], [])

it fails because of a file name collision when staging. If I leave out the second "reads", it will fail because of a null path value. How can I solve this? I feel like a solution is already implemented because the "target" of minimap2 falls back to the reads from the first channel if the reference (the second parameter) is null.

I haven't used minimap in this way, but since the target uses the reads if reference is empty, could you not give it an empty channel?

MINIMAP2_ALIGN(reads, [[],[]], [], [], [], [])

Tried that, but that gives an error:

Path value cannot be null

Hm, looks like there is a similar test https://github.com/nf-core/modules/blob/1d74f91a865c2843f768fe5819369ecbd255b93e/modules/nf-core/minimap2/align/tests/main.nf.test#L118-L150 which seems to work

I made a mistake with the brackets 🙃 Thanks! Now it works