Disable automated trimming by demultiplexing tools.

[grst]

Description of feature

When using an Illumina Samplesheet with Adapters specified in the [Settings] section, bcl2fastq, cellranger mkfastq or BCLconvert automatically perform adapter trimming, e.g.

[Settings],,,,,,,,,,,
Adapter,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA,,,,,,,,,,
AdapterRead2,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT,,,,,,,,,,

I do not think we want to use this feature because

• trimming is done in a separate step using fastp by default, which would result in double-trimming (fastp also reliably auto-detects the adapters, there is no need for storing the adapter sequences).
• trimming might result in issus with single-cell or UMI data. In fact 10x urgently recommends to disable trimming during demux:

I therefore suggest to include a step that removes those lines from the input samplesheets, unless it is specifically disabled via a config flag. This can be achieved e.g. in groovy with a snippet such as

 samplesheet_in
        .readLines()
        .each { line ->
            if ( line =~ /Adapter,[ACGT]+,/ ) {
                line = line.replaceAll(/Adapter,[ACGT]+,/, 'Adapter,,')
            }
            else if ( line =~ /AdapterRead2,[ACGT]+,/ ) {
                line = line.replaceAll(/AdapterRead2,[ACGT]+,/, 'AdapterRead2,,')
            }
            samplesheet_out << line + '\n'
        }

A section should be added to the documentation dedicated to trimming.

CC @apeltzer

[nschcolnicov]

Putting this one on hold until https://github.com/nf-core/demultiplex/issues/209 is closed

[nschcolnicov]

PR for #209 was merged, closing this ticket.