Dear airrflow team, is there any option to alter the behaviour of FASTP when assembling pairs across different airrflow version, like overlap_len_require, overlap_diff_limit and overlap_diff_percent_limit?

Hi @Newton Peres, yes you can provide extra arguments with a configuration file. Just provide the configuration file with the

-c

parameter. E.g.

-c custom.config

, and then specify inside the config the extra arguments for fastp:

process{
  withName:FASTP{
    ext.args = "--disable_quality_filtering --disable_length_filtering --disable_adapter_trimming"
  }
}

Wowww. That was quick! ...and I didn't even pay the premium subscription! 😛 Thank you so much @Gisela Gabernet.