Why are there so few defaults? #

mbf-fastq-processor is following the python mantra ’explicit is better than implicit'.

It’s presumptuous to assume our user’s use case, and mismatches between an assumed and actual use case lead to unwelcome surprises that the user might only discover much later if at all.

Defaults also make for difficult upgrade paths - you can’t really change them later on without silently breaking your user’s outputs (They’ll be different, but it will be not immediately clear to the user why).

Instead have a look at the how-to section.

Empty Reads #

Some of the modifying steps may produce empty reads.

Some downstream aligners, notably STAR, will fail on such empty reads in FastQ files (STAR specifically will complain that sequence length is unequal quality length, even though they’re both 0).

To remove such reads, deploy a FilterEmpty step after the trimming (or a FilterMinLen).