Allow choice of trimmer program

[fgvieira]

Dear all,

not sure if it is supposed to be feature requests in template, but I think it would quite nice to have the option to choose which trimmer to use. For example:

• cutadapt
• fastp
• pear

As I see it, the config could look something like:

trimming:
  activate: false
  tool: cutadapt
  cutadapt:
    # Cutadapt options
    ""
  fastp:
    # Fastp options
    ""
  pear:
    # Pear options
    ""

[christopher-schroeder]

Hey, I can implement this by first creating some snakemake wrappers for fastp and pear. Just because I'm interested: what are the benefits of fastp and pear?

[fgvieira]

I was mostly wondering about the possibility of specifying other adapter programs, since right now the pipeline seems to be pretty much made for cutadapt only (e.g. cutadapt_pipe rule). fastp and pear were just examples of a read trimmer and a read merger for PE, since the latter adds another layer of complexity with a mixture of SE and PE reads that need to be mapped separately and merged. The same applies to some adapter trimming programs, that for PE also output single end reads (if one pair was filtered out), like trimmomatic.

As for the programs, I will probably be interested in several combinations depending on the project:

• adapterremoval: performs read trimming and merging in one step. I've used quite a lot and works fine but can be a bit slow
• fastp or bbduk: seem to be quite fast and have more options (e.g. entropy filtering) and, together with pear, would be equivalent to adapterremoval
• trimmomatic and/or pear: the more "classic" approach for project backward compatibility (if I need to re-run old projects)