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pacsomatic

separate

Prepares and launches nf-core/pacsomatic matched tumor-normal PacBio HiFi genomics workflows from unaligned BAM inputs. Supports samplesheet generation, pinned Nextflow launch artifacts, local checks, LSF/Slurm/PBS Pro/SGE launcher submission, and startup troubleshooting. Use for pacsomatic run preparation and execution, not general short-read somatic analysis or medical imaging PACS.

When to use

• Use [scripts/run_pacsomatic.py](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.…

When not to use

• general short-read somatic analysis
• medical imaging PACS

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