Parallel processing of paired-end fastq files

[PramodRaoB]

From my understanding of the code, in paired-end processing, both fastq input files could be processed parallelly, but they are currently sequential. Is this correct? If so, I could take this feature up.

[FelixKrueger]

Yes, it this is correct. If the trimming could occur in parallel it might indeed speed up the run-time, which sill allowing the the same flexibility further downstream. It might have to be taken care of for resource allocation later on, e.g. on nf-core, but this would be a subsequent step. If you want to have a go at it - that could be nice!