pacsomatic

Editorial and source context

What this Skill does

Pacsomatic is a source-indexed Agent Skill for data, research & analysis work. Based on the SKILL.md description, it focuses on operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from bam inputs. Use the linked GitHub file to confirm scope and prerequisites before enabling it.

What the author says

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.

Compatibility and requirements

• Use an agent runtime that supports Agent Skills and the linked SKILL.md format.
• Confirm the source repository's tools, SDKs, and platform prerequisites for agent workflows work.

How to install or import it

• Open the linked GitHub SKILL.md and review its scope and setup instructions.
• Install or import the skill using the agent runtime's documented workflow.
• Run a small, non-sensitive test and verify the output before broader use.

Permissions and risks

• Review every command, file path, network request, dependency, and credential scope before enabling it.
• GitHub stars indicate popularity, not safety or correctness; validate the source and test with non-sensitive data.

Example workflows

• Ask an AI agent to apply Pacsomatic to agent workflows work described in the source record.
• Have the agent state assumptions, required tools, and expected output before using this data, research & analysis skill.
• Compare the result with the linked GitHub SKILL.md and verify it against your project requirements.