Please support longer insert sizes in paired-end data.

[charles-plessy]

Is your feature request related to a problem? Please describe

My insert size is distributed between 100 and 1000 nt. However, bowtie2's default size for maximum insert size (--maxins parameter) is 500…

Describe the solution you'd like

Could you either pass a max insert size of ~1000 to aligners, or provide an option to override the default ?

Describe alternatives you've considered

I could not find an alternative way of doing this with nf-core/eager.

Additional context

I am using nf-core/eager as simple realignment and QC pipeline for non-ancient DNA, because 1) there is no alternative in nf-core and b) eager is very good for that purpose. Thank you for developing it !

[jfy133]

Yup - should be easiy to add! It will take a little bit of time as the main developers are both swamped with other work, but should get to this in about a week!

[jfy133]

Unless you feel like making a PR of course ;)