This pipeline takes a directory containing paired-end illumina sequence data, plus a reference sequence, aligns the reads against the reference and calls variants. It is based directly off of the excellent Snippy by Torsten Seemann (@tseemann).
nextflow run BCCDC-PHL/call-variants \
--ref <ref.fa> \
--gff <genes.gff> \
--fastq_input </path/to/fastq> \
--outdir <outdir>