pacsomatic

When to use

Use scripts/run_pacsomatic.py to prepare one matched PacBio HiFi tumor/normal pair, generate a samplesheet and reproducible launch artifacts, and launch locally or submit the Nextflow driver to a scheduler. The pipeline realigns input BAMs; this helper targets unaligned HiFi BAMs and optional PacBio .pbi indexes. Do not substitute short reads or treat a BAM filename as evidence of platform, matched identity, or methylation information.

The reviewed upstream dev commit is 24c84cb371b0339c1d65a4de9451671945e19772. GitHub had no releases or tags on 2026-10-01, despite the internal manifest saying 1.0.0. The helper pins that commit by default for nf-core/pacsomatic; it does not invent a release tag. This is a source-reviewed development workflow, not a clinically validated assay. See references/pacsomatic_guide.md for sources and scientific checks.