Is there a reason that

SAMTOOLS_MERGE

supports capturing an outputted

csi

or

crai

index but not a

bai

?

Probably because bai is not the default option with

--write-index

. Started adding an input

val index_format

for lack of a better option (in e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/samtools/view/main.nf). But I think @Maxime Garcia was hoping for a better solution.

you mean for the

unselected_index

?

Personally I feel all the

samtools

modules (and similarly

bcftools

modules) should have the same behaviour for handling indexes where possible, because the usability of

nf-core

modules, especially for newcomers, decreases considerably when such similar modules they have differing interfaces

TOTALLY AGREEING