Add adapter list option

[maxibor]

Give the user the possibility to provide an adapter list

[alexhbnr]

Alternatively, you could rely on a program that allows to have a third adapter sequence that is introduced by the transposase tagmentation step in the Illumina Nextera XT library prep kit. I used trim_galore (https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md), which itself uses cutadapt.

Here some example code:

trim_galore --paired \
                    --quality 10 \
                    --phred33 \
                    --nextera \
                    --gzip \
                    --length 35 \
                    --output_dir {params.outdir} \
                    --basename {wildcards.sample} \
                    --cores {threads} \
                    {input.pe1} {input.pe2}

[maxibor]

AdapterRemoval also has the option to use an file containing a list of adapters --adapter-list

[maxibor]

Now implemented with 51cec64