> ## Documentation Index
> Fetch the complete documentation index at: https://kalarislabs.com/llms.txt
> Use this file to discover all available pages before exploring further.

# pacsomatic — AI agent skill for life sciences

> Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs.

# `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.

**Category:** [life-sciences](/skills#life-sciences) · **License:** MIT · **Version:** 1.2

## Install

```bash theme={null}
npx research-agent-skills install pacsomatic
npx skills add KalarisLabs/research-agent-skills --skill pacsomatic
```

## When to use it

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.

## Full playbook

Read [SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/main/skills/pacsomatic/SKILL.md) for the complete workflow, references and any scripts. The agent installer copies the full skill folder.