kdense-pacsomatic

Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs. Use this skill when the user needs to validate run inputs, generate pacsomatic-compliant samplesheets, prepare reproducible Nextflow launch artifacts, run locally or submit to schedulers (LSF/Slurm/PBS/SGE), and triage execution failures. Triggers on requests to run pacsomatic, prepare launch commands/scripts, perform dry-run checks, or troubleshoot pipeline startup and scheduler submission errors.

Ir a la instalación

Repositorio: eightmm/codex-science
Última actividad en el origen: 10 de julio de 2026 a las 05:18
Idioma detectado de SKILL.md: inglés
Estrellas: 2
Forks: 0

Opciones de instalación

De forma predeterminada está seleccionado el prompt que primero revisa el origen. Puedes cambiar a un comando directo o descargar una copia local.

Instalar con Codex o Claude Copia este prompt, pégalo en Codex, Claude u otro asistente, y deja que revise la página de la skill y la instale por ti.

Un comando directo omite el prompt de revisión. Revisa el origen antes de ejecutarlo.

npx skills add https://github.com/eightmm/codex-science --skill kdense-pacsomatic

El comando permanece en una sola línea. Desplázate horizontalmente para revisarlo antes de copiarlo.

¿Prefieres una copia local? Descarga los archivos que SkillsMP tiene disponibles ahora.

Revisa los archivos de origen

Lee SKILL.md y los archivos complementarios que muestra SkillsMP antes de decidir si quieres instalarlo.

Explorador de archivos

2 archivos

SKILL.md

Instrucciones de origen · Vista previa de solo lectura

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Kdense Pacsomatic

Use this Codex adapter for the pinned upstream scientific skill.

Catalog status

Status: inactive

Source: kdense

Audit reasons: executable-content

Upstream license: MIT

Inventory: ../../inventory.json

Upstream instructions: ../../../vendor/scientific-agent-skills/skills/pacsomatic/SKILL.md

Procedure

Resolve the plugin root as three directories above this skill directory.

Read the matching inventory record and verify its status, reasons, source path, and pinned revision.

Do not read the upstream instructions until the user has seen every audit reason and given explicit acknowledgement. Acknowledgement permits instruction inspection only.

Treat upstream frontmatter as source metadata, not as Codex configuration. Follow the instruction body only where it is compatible with available Codex tools and the current user-approved plan.

Treat tools named for another agent runtime as capability requests. Map them to an available Codex tool only when the behavior is equivalent; otherwise report the unavailable capability.

Ask before credentials, package installation, new network hosts, remote compute, writes, paid services, destructive actions, or imported executable code.

Use $science-provenance for produced scientific outputs and $science-review before presenting scientific claims.

Boundaries

This wrapper does not grant credentials, network access, package installation, or script execution.

Do not change an inactive record to active from inside a research task.

Preserve failures, uncertainty, source identifiers, and licensing constraints.