As noted by @drpatelh, we currently don't follow the current 'standard' within nf-core for specifying by using --paired_end or --single-end exclusively i.e. use one and acts as a logical/boolean parameter.
While I originally did this due to mistrust of novice EAGER users, we should still maintain consistency with other parameters.
To optimise a default, I ran a poll on twitter: https://twitter.com/jafellowsyates/status/1237117020187099139
A majority of groups seem to run paired end sequencing configuration most often.
Therefore I suggest we have --paired_end set to 'true' by default, and therefore remove that flag from user docs and offer only a --single_end flag to override this behaviour.
As noted by @drpatelh, we currently don't follow the current 'standard' within nf-core for specifying by using
--paired_endor--single-endexclusively i.e. use one and acts as a logical/boolean parameter.While I originally did this due to mistrust of novice EAGER users, we should still maintain consistency with other parameters.
To optimise a default, I ran a poll on twitter: https://twitter.com/jafellowsyates/status/1237117020187099139
A majority of groups seem to run paired end sequencing configuration most often.
Therefore I suggest we have
--paired_endset to 'true' by default, and therefore remove that flag from user docs and offer only a--single_endflag to override this behaviour.