--max_n value as a fraction

[bounlu]

--max-n parameter in cutadapt accepts a fraction of read length in addition to the number of Ns, however, trim_galore seems to only accept as counts for this parameter. How to make trim_galore compatible with the fraction? What happens if I pass a value of fraction to trim_galore?

trim_galore:

--max_n COUNT           The total number of Ns (as integer) a read may contain before it will be removed altogether.
                        In a paired-end setting, either read exceeding this limit will result in the entire
                        pair being removed from the trimmed output files.

cutadapt:

--max-n COUNT           Discard reads with more than COUNT 'N' bases. If COUNT is a number between 0 and 1,
                        it is interpreted as a fraction of the read length.

[FelixKrueger]

I suppose this shouldn't be too hard to implement, is this something you would require?

[FelixKrueger]

I have now had a go at implementing this (e6ed90a), can you try and clone the dev branch and see if it works for you?

[bounlu]

Really appreciate the quick effort, however I have switched to cutadapt for more flexible options overall.

[FelixKrueger]

That's fine, maybe someone else will want it at some point.