Oropharyngeal resistome nextflow pipeline

Usage

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

sample,fastq_1,fastq_2
CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz

Each row represents a pair of fastq files (paired end).

 nextflow run greninger-lab/oropharyngeal_resistome -r main -latest \
                --input samplesheet.csv  \
                --outdir /path/to/out/  \
                --ref CP039887.fasta  \
                --card_ref /path/to/unique/appended/rownum/CARD/card_database_v3.2.9_rownum_all.fasta  \
                --rgi_card_path /path/to/rgi/db/CARD  \
                --kraken_host_db /path/to/host/db/Kraken2_human/k2_human/  \
                -profile docker  \