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pacsomatic Tumor-Normal Workflow Helper

Prepares and launches nf-core/pacsomatic tumor-normal PacBio HiFi analyses with checks and scheduler submission

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
6 files

What it does

When installed, the agent can set up a matched tumor and normal PacBio HiFi genome analysis run using the nf-core/pacsomatic pipeline. It checks inputs, generates a samplesheet and reproducible launch files (a params YAML and a script), and can launch the Nextflow workflow locally or submit it to a cluster scheduler such as Slurm, LSF, PBS Pro or SGE. It also helps troubleshoot startup problems. It is meant for pacsomatic runs specifically, not general short-read cancer analysis or medical imaging PACS systems.

Great for

  • Bioinformaticians preparing matched tumor/normal PacBio HiFi runs on an HPC cluster
  • Research groups who already have unaligned HiFi BAM files and want reproducible Nextflow launch artifacts
  • Operators who need a dry-run review step before submitting a pipeline job

Skip it if

  • Short-read sequencing data or general somatic analysis, because the skill is scoped to pacsomatic and HiFi BAMs (wrong platform gives wrong results)
  • Clinical diagnosis or patient care, because the skill itself states it is a source-reviewed development workflow and not a clinically validated assay
  • Medical imaging or hospital PACS archives, which share the acronym but are unrelated

Try asking

  • “Prepare a dry-run pacsomatic setup for tumor BAM /data/P001_T.bam and normal BAM /data/P001_N.bam using GRCh38.fa”
  • “Generate the samplesheet and params files for patient P001 without launching anything yet”
  • “Submit a reviewed pacsomatic run to our Slurm queue with 2 CPUs, 8 GB memory and a 48-hour walltime”
  • “Help me diagnose why my Nextflow pacsomatic launch failed at startup”
Step-by-step guide: how to use pacsomatic Tumor-Normal Workflow HelperInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 6 original files, the MIT licence and an attribution note.

    pacsomatic.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip pacsomatic.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip pacsomatic.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Always run with --dry-run first and review the generated samplesheet, params YAML and script before using --run or --submit
  • Load cluster modules and choose the runtime (--use-current-path or --conda-env) yourself before invoking the helper; keep signed URLs and secrets out of generated files
  • Treat scheduler acceptance as the start, not the end: check pipeline QC outputs and keep the output directory stable so --resume works

What's inside

  • config.yaml
  • references/agent-playbook.md
  • references/config-and-output.md
  • references/pacsomatic_guide.md
  • scripts/run_pacsomatic.py
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.