Cutdapt for batch processing ?

Question

[sunnykevin97]

HI

I had around 100 fastq files to be preprocessed wish to use cutadapt for removing adapters. How I do as a batch in one go. Suggestions please.

[Nicolas Rosewick]

what did you try ? start maybe by a combination of ls and xargs ?

[GenoMax]

Please search biostars in future (use google search since the built in search does not work that well):
cutadapt loop and paired-end reads
C: Bash Script Loop Help

Answer 1

[Asaf]

Use pipeline management system like nextflow, snakemake or wdl/cromwell.

And make sure you have to actually use cutadapt. If your next step is mapping to the genome you're probably good without removing adapters.