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.
npx skills add BioTender-max/awesome-bio-agent-skills --skill pacsomatic --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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-le
- Overview
- When to Use This Skill
- Routing and Execution Rules
- Inputs Required
- Workflow
- Agent Response Contract
- Quick Start
- Configuration
- Testing
- References
python scripts/run_pacsomatic.py \ python -m unittest discover -s tests -v
What does the pacsomatic skill do?
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.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill pacsomatic --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.