nextflow run Figaro \
--ontAmplicon \
--inDir <input directory> \
--outDir <output directory> \
--reference <reference.fasta> \
--primer <primer bed file> \
--medakaModel <medaka model>
| Parameter | Description |
|---|---|
| inDir | directory containing sub-directories with non-concatenated fastq files or directory containing concatenated fastq files |
| reference | custom reference, e.g. whole genome or pol gene only |
| primer | bed file used for primer trimming. See sample assets/primers/primerpair_pol.bed. If primers are not within the reference fasta, just use 0 for the genomic range in the bed file. |
| medakaModel | see list |
nextflow run Figaro \
--illuminaShotgun \
--inDir <input directory > \
--outDir <output directory>
| Parameter | Description |
|---|---|
| inDir | directory containing the forward and reverse fastq files |
Download xml files here then revise --sierraXML in the nextflow.config.