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pacsomatic

k-dense-ai/scie…t-skills

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.

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安装命令

npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill pacsomatic

SKILL.md

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.

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.

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