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pacsomatic Run Operator

Validates inputs, generates pacsomatic samplesheets and launch artifacts, then runs or submits nf-core/pacsomatic tumor-normal analyses locally or on HPC schedulers.

AutomationAdvanced★ 33,030⑂ 3,248AI score 8/10Last updated: Aug 9, 2026

What it does

  • Validates required inputs: tumor/normal BAM paths, patient and sample IDs, output directory, and exactly one reference mode (--fasta or --genome).
  • Generates a pacsomatic-compliant samplesheet (patient,sample,status,bam,pbi), a params YAML, and a reusable launch script for reproducible reruns.
  • Supports --dry-run validation-only checks or --run for local execution and LSF/Slurm/PBS/SGE submission, returning the detected job ID.
  • On failure, reports the first failure point and the next triage target (.nextflow.log, pipeline_info, failing task logs).

Who it's for

  • Genomics researchers running matched tumor-normal variant analysis with nf-core/pacsomatic.
  • Bioinformatics engineers and core facilities repeatedly submitting pipelines to HPC schedulers.
  • Anyone who prefers reproducible artifacts over hand-assembled nextflow run commands.

Example uses

  1. "Do a dry run for this tumor-normal pair and tell me what's missing" → validates paths, IDs, and reference mode, then emits artifacts only.
  2. "Submit to Slurm on queue compute with 16 CPUs, 64GB, 48h and give me the job ID" → builds the launch script, submits, and reports the job ID.
  3. "Why did the pacsomatic submission fail?" → pinpoints the first failure and the next log to inspect.

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/pacsomatic/SKILL.md

What I want: (describe your task here)

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↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/pacsomatic folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/pacsomatic/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/pacsomatic ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open a terminal and change into your working directory.
  2. Clone the repo: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  3. Create the skills directory: mkdir -p ~/.claude/skills
  4. Copy just this skill: cp -r scientific-agent-skills/skills/pacsomatic ~/.claude/skills/
  5. Make sure prerequisites are available: Java, Nextflow, a container runtime (Singularity/Docker), and Python 3.
  6. Restart Claude Code and ask something like "prepare a pacsomatic dry run" to confirm the skill activates.
  7. Optional: run python -m unittest discover -s tests/pacsomatic -v from the skill root to verify the helper script works.
View source on GitHub ↗License: MIT