Individual skill
pacsomatic
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.
skills/pacsomatic/SKILL.md
Source commit 2d2065fb4520fa3f3f2bcf61cff26ec8b7eba4b5
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- Last checked
- Nov 10, 2026
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- Repository last updated
- Nov 9, 2026
- License
- MIT
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- ai-scientist Repository topic
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LICENSEasset · 1,068 bytesSKILL.mdcore · 6,477 bytesSKILL.mdcore · 6,477 bytesSKILL.mdcore · 6,477 bytesconfig.yamlasset · 1,060 bytesreferences/agent-playbook.mddoc · 2,045 bytesreferences/config-and-output.mddoc · 5,984 bytesreferences/pacsomatic_guide.mddoc · 5,340 bytesscripts/run_pacsomatic.pyruns · 36,728 bytes
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# pacsomatic
## 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.
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