name: Cutadapt
description: cutadapt removes adapter sequences from high-throughput sequencing reads
keywords:
    - Quality Control
    - QC
    - Adapters
tools:
    - fastqc:
        description: |
            Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence
            from your high-throughput sequencing reads.
            
            Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the 3’
            sequencing adapter because the read is longer than the molecule that is sequenced. Amplicon reads 
            start with a primer sequence. Poly-A tails are useful for pulling out RNA from your sample, but 
            often you don’t want them to be in your reads.
        homepage: https://cutadapt.readthedocs.io/en/stable/
        documentation: https://cutadapt.readthedocs.io/en/stable/
input:
    -
        - sample_id:
            type: string
            description: Sample identifier
        - reads:
            type: file
            description: Input FastQ file, or pair of files
output:
    -
        - sample_id:
            type: string
            description: Sample identifier
        - reads:
            type: file
            description: trimmed FastQ file, or pair of files
authors:
    - @piotr-faba-ardigen