pacsomatic

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.”