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.
- Version
- 1.2
- License
- MIT
Pinned to revision 70a605012eee, so it is the text this page describes rather than whatever the author pushed since.
Files
- skills/pacsomatic/SKILL.md
- skills/pacsomatic/LICENSE
- skills/pacsomatic/config.yaml
- skills/pacsomatic/references/agent-playbook.md
- skills/pacsomatic/references/config-and-output.md
- skills/pacsomatic/references/pacsomatic_guide.md
- skills/pacsomatic/scripts/run_pacsomatic.py
Every link opens the file at its source, pinned to the revision this page describes.