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Agent skill

Pacsomatic

by BioTender-max in BioTender-max/awesome-bio-agent-skills

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

MITAuto-check passedResearch & Science

Install Pacsomatic

skills CLI
$ npx skills add BioTender-max/awesome-bio-agent-skills --skill pacsomatic -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install BioTender-max/awesome-bio-agent-skills pacsomatic --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/BioTender-max/awesome-bio-agent-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/kdense/pacsomatic .claude/skills/pacsomatic && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
pacsomatic
GitHub stars
197
Token cost
~1.3k tokens
SKILL.md length
454 words
Files
8 (incl. scripts, references)
Skills in repo
18
Repo updated
First seen
Licence
MIT

At a glance

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

  • Works in 6 steps: Always collect required run inputs first. → Always route through… → Default to --dry-run when the user asks… → …
  • The user needs to validate run inputs
  • SKILL.md covers Overview, When to Use This Skill, Routing and Execution Rules and Inputs Required, plus 6 more sections
  • Runs Python scripts from its folder; calls python

What it does

Pacsomatic is an agent skill from BioTender-max/awesome-bio-agent-skills. 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.

Its SKILL.md is about 1.3k tokens, which your agent loads only when the skill is triggered. The skill folder holds 10 other files, including scripts and reference files (for example `config.yaml`, `references/agent-playbook.md` and `references/config-and-output.md`).

It sits in Research & Science, covering Reproducible research. It works with Nextflow. The repository describes itself as: A curated collection of AI agent skills for biomedical research, covering genomics, proteomics, single-cell analysis, clinical AI, and protein design. The licence is MIT.

When your agent uses it

  • The user needs to validate run inputs
  • Generate pacsomatic-compliant samplesheets
  • Prepare reproducible Nextflow launch artifacts
  • Submit to schedulers (LSF/Slurm/PBS/SGE)

Example prompts

  • “/pacsomatic”

Requirements

  • Python 3

Workflow steps

6 steps, taken from the first numbered list in SKILL.md.

  1. Always collect required run inputs first.
  2. Always route through scripts/run_pacsomatic.py for validation and artifact generation.
  3. Default to --dry-run when the user asks for checks/validation only.
  4. Use --run only when the user asks to execute/submit.
  5. For scheduler modes, include executor-specific resource arguments and return detected job ID when available.
  6. If execution fails, report first failure point and next triage target (.nextflow.log, pipeline_info, failing task logs).

What it can do on your machine

Read from SKILL.md and the folder at commit 8cbdd18. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships 1 file in scripts/ (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Pacsomatic loads about 1.3k tokens when it runs, and up to ~4.2k if it reads all its reference files. Until then it costs about 125 tokens; SKILL.md has 454 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~125
When it runs · the whole SKILL.md, loaded when a task matches
~1.3k
With references · SKILL.md plus every file in references/, read only if the agent opens them
~4.2k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from BioTender-max/awesome-bio-agent-skills at commit 8cbdd18, republished under its MIT licence (© BioTender-max). 454 words, ~1,257 tokens.

Download SKILL.mdSave it as .claude/skills/pacsomatic/SKILL.md (or your agent's skills folder). This skill also uses 7 other files; get the full folder from GitHub.
name
pacsomatic
description
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.
license
MIT
metadata.skill-author
Beifang Niu
metadata.contributors
Haidong, Wenchao
metadata.upstream-pipeline
https://github.com/nf-core/pacsomatic

pacsomatic

Overview

This skill provides a reproducible execution workflow for nf-core/pacsomatic, centered on a single helper entrypoint that handles validation, artifact generation, and optional execution.

Primary entrypoint:

  • scripts/run_pacsomatic.py

The helper script:

  • validates required identifiers, files, reference mode, and runtime prerequisites
  • writes a pacsomatic-compatible samplesheet (patient,sample,status,bam,pbi)
  • generates a params YAML and launch script for reproducible reruns
  • supports dry-run validation and run/submit execution paths

Use this skill as the default path for pacsomatic operations. Do not bypass it with manually assembled nextflow run nf-core/pacsomatic commands unless the user explicitly asks for manual command construction.

When to Use This Skill

Invoke this skill when the user asks to:

  • run matched tumor-normal analysis from BAM files
  • generate or fix pacsomatic samplesheet and launch artifacts
  • execute locally or submit to schedulers (LSF/Slurm/PBS/SGE)
  • perform dry-run validation before execution
  • troubleshoot launch failures or summarize run outputs

Do not use this skill for:

  • deep biological interpretation beyond run-level sanity checks
  • editing pipeline internals unless explicitly requested

Typical trigger phrases:

  • "run nf-core/pacsomatic for this tumor-normal pair"
  • "prepare pacsomatic samplesheet and launch script"
  • "do a dry run first and tell me what is missing"
  • "submit pacsomatic to slurm/lsf and return the job id"
  • "why did pacsomatic submission fail"

Routing and Execution Rules

  1. Always collect required run inputs first.
  2. Always route through scripts/run_pacsomatic.py for validation and artifact generation.
  3. Default to --dry-run when the user asks for checks/validation only.
  4. Use --run only when the user asks to execute/submit.
  5. For scheduler modes, include executor-specific resource arguments and return detected job ID when available.
  6. If execution fails, report first failure point and next triage target (.nextflow.log, pipeline_info, failing task logs).
Show full SKILL.md (182 more words)Show less

Inputs Required

Required:

  • tumor BAM path
  • normal BAM path
  • patient ID
  • tumor sample ID
  • normal sample ID
  • output directory
  • exactly one reference mode: --fasta or --genome

Optional:

  • profile, resources, scheduler account/queue
  • pipeline version (-r)
  • params file, resume/report/dag flags
  • --dry-run and/or --run

Workflow

  1. Validate identity and input constraints.
  2. Validate required local paths (BAM, optional PBI, optional FASTA).
  3. Resolve runtime and dependency checks.
  4. Build samplesheet and generated params YAML.
  5. Generate launch script for selected executor.
  6. If --dry-run and not --run, stop after artifact generation.
  7. If --run, execute locally or submit to scheduler.
  8. Return command/script path, validation status, and job ID (if detected).

Agent Response Contract

Every response after invocation should include:

  • exact command used or generated script path
  • confirmation that validation checks ran
  • run type (dry-run vs run)
  • scheduler job ID when available
  • one concrete next step for validation/triage

Quick Start

Dry run:

bash
python scripts/run_pacsomatic.py \
  --tumor-bam /path/to/tumor.bam \
  --normal-bam /path/to/normal.bam \
  --patient-id P001 \
  --tumor-sample-id P001_T \
  --normal-sample-id P001_N \
  --outdir /path/to/output \
  --genome GRCh38 \
  --profile singularity,sanger \
  --dry-run

Scheduler execution example (Slurm):

bash
python scripts/run_pacsomatic.py \
  --tumor-bam /path/to/tumor.bam \
  --normal-bam /path/to/normal.bam \
  --patient-id P001 \
  --tumor-sample-id P001_T \
  --normal-sample-id P001_N \
  --outdir /path/to/output \
  --genome GRCh38 \
  --profile singularity,sanger \
  --executor slurm \
  --queue compute \
  --project my_account \
  --cpus 16 \
  --memory-gb 64 \
  --walltime 48:00 \
  --run

Configuration

Use config.yaml as the baseline for profile/executor/runtime defaults. Override at invocation time when user requirements differ.

Testing

Run unit tests from skill root:

bash
python -m unittest discover -s tests -v

References

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

© BioTender-max, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 7 other files (scripts, references) in skills/kdense/pacsomatic of BioTender-max/awesome-bio-agent-skills.

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

Open the folder on GitHubat commit 8cbdd18

Compare with similar skills

Pacsomatic next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Pacsomatic compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Pacsomatic this skillBioTender-max/awesome-bio-agent-skills197—~1.3kAutomated safety check: PassMIT
Add Bactopia Toolbactopia/bactopia522—~4.1kAutomated safety check: PassMIT
Bump Versionsbactopia/bactopia522—~1.3kAutomated safety check: PassMIT
Merge Schemasbactopia/bactopia522—~1.3kAutomated safety check: PassMIT
LaminDB Biological Data Managementdavila7/claude-code-templates32k12 repos~3.6kAutomated safety check: PassMIT
Latchbio Integrationdavila7/claude-code-templates32k11 repos~2.4kAutomated safety check: PassMIT

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Works with

Categories

Questions about Pacsomatic

What does Pacsomatic do?

Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs. Pacsomatic is an agent skill from BioTender-max/awesome-bio-agent-skills. Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs.

When should I use Pacsomatic?

Pacsomatic fits situations like: the user needs to validate run inputs; generate pacsomatic-compliant samplesheets; prepare reproducible Nextflow launch artifacts; submit to schedulers (LSF/Slurm/PBS/SGE).

How do I install Pacsomatic in Claude Code?

Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill pacsomatic -a claude-code`. Or copy the skill folder (skills/kdense/pacsomatic in BioTender-max/awesome-bio-agent-skills) into .claude/skills/pacsomatic in your project. Claude Code loads it when a task matches its description.

How do I install Pacsomatic in Codex?

Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill pacsomatic -a codex`. Or copy the skill folder (skills/kdense/pacsomatic in BioTender-max/awesome-bio-agent-skills) into .agents/skills/pacsomatic in your project. Codex loads it when a task matches its description.

Can I use Pacsomatic in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add BioTender-max/awesome-bio-agent-skills --skill pacsomatic -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/pacsomatic, .gemini/skills/pacsomatic, .github/skills/pacsomatic and .opencode/skills/pacsomatic in your project.

What does Pacsomatic need to run?

Going by SKILL.md and its folder, Pacsomatic needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.

Does Pacsomatic access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Pacsomatic safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Pacsomatic use?

Pacsomatic is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Pacsomatic use?

About 1.3k tokens (SKILL.md is roughly 5k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 2.9k tokens, read only when the agent opens those files.

What are the alternatives to Pacsomatic?

Skills that share tags, products or a category with Pacsomatic: Add Bactopia Tool (bactopia/bactopia, 522 stars), Bump Versions (bactopia/bactopia, 522 stars), Merge Schemas (bactopia/bactopia, 522 stars) and LaminDB Biological Data Management (davila7/claude-code-templates, 32k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Pacsomatic?

BioTender-max (a GitHub user) maintains it in BioTender-max/awesome-bio-agent-skills, which has 197 GitHub stars. The repository holds 18 skills in this directory. The repository was last updated on July 1, 2026.

Source: BioTender-max/awesome-bio-agent-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.