DSL2 - Host-removal keeps adapters in [DISCUSSION?]

[merszym]

Status Quo

Host removal is a process to create fasta/fastq files (for ENA) without the host DNA. Currently, the fasta that go into the host removal process are the non-preprocessed reads (unmerged, not adapter-clipped)

ch_fastqs_for_host_removal = ch_fastqs_for_preprocessing.map { meta, fastqs ->
            new_meta = meta.clone().findAll { it.key !in ['lane', 'colour_chemistry', 'single_end'] }
            [new_meta, meta, fastqs]
        }

Problem

Fasta-files for ENA should not contain adapters (see https://ena-docs.readthedocs.io/en/latest/submit/fileprep/reads.html)

Solution

Use the ch_reads_for_mapping channel as input for Host Removal instead, the user can then decide to keep the adapters in by setting the --skip_preprocessing flag.

[merszym]

Maybe related to #974