skills.rest
jasrajtulsi
jasrajtulsiCOMMUNITY
Explore all skills by this author →
GitHub

pacsomatic

Validates tumor-normal BAM inputs and prepares launch artifacts for nf-core/pacsomatic across LSF, Slurm, PBS, SGE.

Updated Jul 1, 2026
Search Tags:#bioinformatics#dry run#nextflow#scheduler#samplesheet#pacsomatic
One-click install
npx skills add https://github.com/jasrajtulsi/GRAD-SCOPE --skill pacsomatic-jasrajtulsi
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pacsomatic
Source: https://github.com/jasrajtulsi/GRAD-SCOPE/tree/main/.claude/skills/pacsomatic
Command: npx skills add https://github.com/jasrajtulsi/GRAD-SCOPE --skill pacsomatic-jasrajtulsi

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill removes the manual friction of preparing and launching nf-core/pacsomatic analyses from matched tumor and normal BAM inputs, helping operators validate inputs, build reproducible launch artifacts, and avoid common setup mistakes.

Core Features & Use Cases

  • Input validation: Checks patient and sample identifiers, BAM paths, optional index files, and the required choice of either a FASTA reference or a genome key.
  • Launch preparation: Generates a pacsomatic-compatible samplesheet, a generated parameter file, and a ready-to-run launch script.
  • Execution support: Handles dry runs, local execution, and scheduler submission for LSF, Slurm, PBS, and SGE.
  • Troubleshooting workflow: Surfaces missing runtime tools, warns about dependency gaps, and reports the submitted job ID when available.

Quick Start

Ask the pacsomatic skill to validate your tumor and normal BAM inputs, choose either a FASTA reference or a genome key, generate the launch artifacts, and perform a dry run or submission as needed.

Frequently Asked Questions about pacsomatic

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

FAQPage Schema
How do I validate matched tumor-normal BAM inputs for an nf-core pipeline?▼

To validate matched tumor-normal BAM inputs, checks are performed on patient and sample identifiers, BAM file paths, and optional index files to ensure they meet pipeline requirements before launch.

How do I submit nf-core jobs to a Slurm or LSF scheduler?▼

You can submit nf-core jobs to LSF, Slurm, PBS, or SGE schedulers by generating a ready-to-run launch script that handles scheduler submission and reports the submitted job ID.

Do I need a FASTA reference file or a genome key to run a pacsomatic analysis?▼

A pacsomatic analysis requires choosing either a FASTA reference file or a genome key for reference-mode selection, and input validation will fail if neither is provided.

What is included in the launch artifacts for a Nextflow dry run?▼

Launch artifacts for a Nextflow dry run include a pacsomatic-compatible samplesheet, a generated parameter file, and a ready-to-run launch script for execution or scheduler submission.

Why does my bioinformatics pipeline submission fail due to missing dependencies?▼

Pipeline submission may fail due to missing runtime dependencies; the workflow surfaces missing tools, warns about dependency gaps, and checks the environment before attempting execution.

Related Skills

Explore More Software Engineering Skills→
dralkhdralkh
74

pacsomatic

Generate validated nf-core/pacsomatic samplesheets and launch scripts from tumor-normal BAM inputs.

Community
Advanced
SheshiyerSheshiyer

pre-launch-email-sequence

Generate and schedule pre-launch announcement and reminder emails with JSON handoff.

Community
Basic
danilomongedanilomonge
1

metapep

Orchestrate nf-core/metapep pipeline runs for reproducible epitope predictions from metagenomic samples.

Community
Advanced
galeepgaleep

pacsomatic

Automate matched tumor-normal workflow analysis from BAM inputs using nf-core/pacsomatic.

Community
Advanced