Preprocessing: Add porechop for Nanopore data

[sofstam]

Feature

PCR adaptors and low quality bases need to be removed.

What needs to be done

Porechop is not currently maintained but a lot of nf-core pipelines are still using it and it is already implemented as nf-core module porechop

Add preprocessing steps for Nanopore reads for removal of PCR adaptors and low quality bases.

This can be closed when

• [x] Evaluate the which software that is optimal for trimming (porechop is currently used by nf-core)
• [x] Add porechop/alternative to process the fastq files after the FastQC step

[sofstam]

@ljmesi I guess I can close this one, right? We can evaluate the alternative to porechop later in the development.

[ljmesi]

Hi @sofstam, Sorry for late reply! I was on holiday until now. Yes, we can close this.