Agent skill · software engineering · k-dense-ai
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.
Why this skill is useful
Adds a comprehensive executable script for validating and running nf-core/pacsomatic workflows that includes error handling and artifact generation.
What it needs
Requires nextflow, python installed locally. About 3k tokens when loaded. Last updated 2026-08-03. 32,849 stars on the source repository.
What this skill does
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/runpacsomatic.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/runpacsomatic.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. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills k-dense-ai/pacsomatic