The pipeline writes per-sample, per-amplicon IGV reports to:
results/<sample_id>/<amplicon>/igv_report/<sample_id>.<amplicon>.igv_report.html
The IGV report module uses the called VCF as the site table and includes both the VCF and BAM as IGV tracks. Report padding can be changed with --igv_report_flanking. Set --igv_report_standalone true to ask igv-reports to embed JavaScript in the HTML report.
nextflow run main.nf -profile slurm --samplesheet samplesheet.tsv --threads 8