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 indexes. Do not substitute short reads or treat a BAM filename as evidence of platform, matched identity, or methylation information. The reviewed upstream commit is . GitHub had no releases or tags on 2026-10-01, despite the internal manifest saying . The helper pins that c…