Unaligned interleaved CRAM output

[vinjana]

Currently, only single-end read files are produced, e.g. one for each of r1, r2, etc. Another common format is interleaved format, in which matching reads are written as continuous sequence into a single file.

nf-core uses unaligned interleaved CRAM. We should be able to produced these files.

For the start, just consider read-pairs, but ignore issues about e.g. r3, r4, i1, i2, etc. files.