Basic Nextflow pipeline script to detect antibiotic resistance using NGS data.
Tested only with single-read Illumina fastq files present in one folder (e.g. 'rawdata')
Using modules:
- fastp for fastq files trimming.
- fasqc for fastq quality control.
- srst2 for antibiotic resistance prediction (https://github.com/katholt/srst2#output-files).
Using Singularity images from
https://depot.galaxyproject.org/singularity/
Using Antibiotic Resistance gene cards from
https://github.com/katholt/srst2/blob/master/data/CARD_v3.0.8_SRST2.fasta
Usage:
nextflow Antib_res_pipeline.nf --indir <rawdata> --ref_gen CARD_v3.0.8_SRST2.fasta -profile singularity
sample result folder in "saved_results"