Pass file to cutadapt

[morriso1]

Description of feature

Thanks for developing this useful pipeline.

I was wondering if it's possible to run the screening pipeline with cutadapt specifying fasta file of multiple adaptor sequences e.g. like here. I have tried trying to pass --cutadapt file:adapters.fasta to the nextflow pipeline, however, I receive an error stating that the 'adapters.fasta' file cannot be found, even though it is there locally.

I am running nextflow version 23.10.1, crisprseq v2.1.1, with singularity as a profile.

Thanks for your help.

[LaurenceKuhl]

Hi @morriso1 that's a very fair request thanks a lot for pitching it! I'll look into it and get back to you!

[LaurenceKuhl]

Hi @morriso1, out of curiosity, do you use an aligner after running your samples through cutadapt? I'm trying to implement bowtie2 in the pipeline but since don't have any working example, i thought i'd reach out to see if it's a step you've ever done.
Best,
Laurence