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gabrielvuksani
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pacsomatic

Validate tumor-normal BAM inputs and generate pacsomatic samplesheets, params YAML, and scheduler launch scripts.

Updated Aug 23, 2026
Search Tags:#nf-core#nextflow#samplesheet#dry-run validation#pacsomatic#tumor-normal#hpc scheduler
One-click install
npx skills add https://github.com/gabrielvuksani/wotann --skill pacsomatic
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pacsomatic
Source: https://github.com/gabrielvuksani/wotann/tree/main/skills/scientific/pacsomatic
Command: npx skills add https://github.com/gabrielvuksani/wotann --skill pacsomatic

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

It solves the problem of preparing matched tumor-normal inputs for nf-core/pacsomatic in a reproducible way without manually assembling fragile samplesheets, parameters, and scheduler launch details.

Core Features & Use Cases

  • Input validation & guardrails: Checks patient/sample ID formatting, verifies BAM/optional .pbi paths (and warns when BAM indexes are missing), and enforces exactly one reference mode (fasta or genome).
  • Reproducible artifact generation: Produces a pacsomatic-compliant samplesheet (patient,sample,status,bam,pbi), generates a params YAML for repeatable runs, and writes an executor-specific launch script.
  • Dry-run, local run, or scheduler submission: Supports generate-only, validation-only via dry-run, and execution/submission via local, LSF, Slurm, PBS, or SGE, including job-id detection and failure triage pointers.

Quick Start

Use the pacsomatic skill to generate a verified samplesheet and launch script for a tumor/normal BAM pair by running the request “Run nf-core/pacsomatic for this tumor-normal pair and do a dry run, using genome GRCh38, and place outputs in /path/to/output.”

Frequently Asked Questions about pacsomatic

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I generate a samplesheet for nf-core pacsomatic tumor-normal runs?▼

To generate a pacsomatic samplesheet, you provide matched tumor-normal BAM inputs and the skill validates patient/sample IDs, checks BAM paths, and outputs a compliant samplesheet with patient, sample, status, bam, and pbi columns.

What's the best way to submit nf-core pacsomatic jobs to an HPC scheduler?▼

Submitting pacsomatic jobs to HPC schedulers is handled by generating executor-specific launch scripts that support LSF, Slurm, PBS, or SGE, including automatic scheduler job ID detection and failure triage pointers after submission.

Can I do a dry-run validation for nf-core pacsomatic before executing the pipeline?▼

Yes, you can perform a dry-run validation for nf-core pacsomatic to verify inputs and parameters without executing the pipeline, ensuring your tumor-normal BAM inputs and reference modes are correctly configured before submission.

Do I need a specific reference mode to run nf-core pacsomatic?▼

You must enforce exactly one reference mode for nf-core pacsomatic by specifying either a FASTA file or a genome build, ensuring the pipeline has the correct genomic reference data for your tumor-normal analysis.

Why does my pacsomatic Nextflow run fail when BAM indexes are missing?▼

Missing BAM indexes cause pacsomatic validation failures because the skill checks for optional .pbi index files alongside BAM inputs and warns when they are absent, preventing execution with incomplete alignment data.

Does pacsomatic support generating a params YAML for reproducible Nextflow execution?▼

Yes, pacsomatic supports generating a params YAML file that captures your run configurations, ensuring reproducible Nextflow execution artifacts alongside the generated samplesheet and executor-specific launch scripts.

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