pacsomatic
K-Dense-AI/scientific-agent-skills
This skill provides a comprehensive and reproducible execution workflow for matched tumor-normal pair analyses using the nf-core/pacsomatic pipeline. It manages the entire process, including input validation (BAM files), generating pacsomatic-compliant samplesheets, creating reproducible launch artifacts (params YAML), and supporting execution submission to various schedulers (Slurm, LSF, PBS). Use this skill for dry-run validation, local execution, or job submission, ensuring consistent and traceable results.