Order of execution? about fastp

[sklages]

Example trimming:

I want to trim my PE dataset like this:

• trim quality at 3' end
• trim poly G and poly A at 3' end
• finally trim 10 bases from both ends 5' and 3' of read pair
  .. order is important.

Theoretically I could do this in just one single call of fastp. In practice I need to know the order of execution of the individual steps.

Alternatively I would need to run trimming in two or more separate processes like this to force a certain order of execution:
fastp <quality/polyX params> | fastp <cut bases at all ends params> or something similiar. ut that would probably reduce speed ...

Any thoughts on that?

thanks :-)

[sklages]

@sfchen This is relevant again :-)

[sklages]

OK, it's described in the README and - due to the hardcoded order - forces my workflow to be split in two separate fastp jobs .. not optimal :-(