pacsomatic
Prepares and launches nf-core/pacsomatic matched tumor-normal PacBio HiFi genomics workflows from unaligned BAM inputs. Supports samplesheet generation, pinned Nextflow launch artifacts, local checks, LSF/Slurm/PBS Pro/SGE launcher submission, and startup troubleshooting. Use for pacsomatic run preparation and execution, not general short-read somatic analysis or medical imaging PACS.
- Version
- 1.4
- License
- MIT
- Compatibility
- Requires Python 3.10+ for the standard-library helper. Execution requires Bash, Nextflow >=24.04.2, a compatible Java runtime (current Nextflow supports Java 17-26), the selected container runtime and optionally a scheduler. Network access is needed for uncached pipeline code, plugins, references and containers.
Pinned to revision 68105dd992f1, 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/SKILL_CN.md
- 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.