nf_trim_fastq

The workflow trims fastq files for adapter content etc. using fastp.

https://github.com/OpenGene/fastp

It then runs fastqc on the trimmed files to generate quality control reports, and gathers both the fastqc and fastp reports into a single report using multiqc.

https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

https://multiqc.info/

Usage

nextflow run crukci-bioinformatics/nf_trim_fastq

Conda environment

The workflow uses a conda environment to manage dependencies. The environment file is conda.yaml.

Input

The workflow expects a directory containing fastq files. The directory should be specified using the --inputDir parameter. By default, the workflow expects the fastq files to be in a directory called fastq in the current working directory.

Additional parameters are:

• --outputDir - the directory to write the trimmed fastq files to. By default, the trimmed files and reports are written to a directory called fastq_trimmed in the current working directory.
• --fastqPattern - a glob pattern to match the fastq files. By default, the workflow will match files ending in r_{1,2}.fq.gz. The r_{1,2} part of the pattern detects the read 1 and read 2 files of paired end data.
• --fastpOptions - additional options to pass to fastp. By default, the workflow uses:

    --detect_adapter_for_pe \
    -g \
    -x