Alternative specification of FASTQs and read structures

[nh13]

Description of feature

See original discussion: #38 (comment)

Currently the pipeline requires a list of FASTQs and a list of read structures, where the order matters. Could we consider more explicit alternatives that could be added in addition to the current way to specify them?

E.g. eExplicitly named fastq/read-structure pairs. We could use names like R1, R2, I1(i7), and I2(i5)