Generate validated nf-core/pacsomatic samplesheets and launch scripts from tumor-normal BAM inputs.
npx skills add https://github.com/dralkh/seerai --skill pacsomatic-dralkh
Please help me install this Agent Skill. Skill: pacsomatic Source: https://github.com/dralkh/seerai/tree/main/skills/pacsomatic Command: npx skills add https://github.com/dralkh/seerai --skill pacsomatic-dralkh
pacsomatic removes the manual friction of preparing and launching matched tumor-normal somatic analysis runs, giving operators a validated path from BAM inputs to reproducible Nextflow execution.
Ask the pacsomatic skill to validate your matched tumor-normal BAM inputs, generate the samplesheet and launch script, and prepare a dry-run or scheduler submission with the reference mode you want.
High-intent search queries and answers about installing and using this skill.
To validate matched tumor-normal BAM inputs for PacBio somatic analysis, provide patient and sample identifiers alongside tumor and normal BAM paths. The skill checks file paths, reference mode, and available runtime prerequisites before generating launch assets.
Yes, you can run nf-core pacsomatic on Slurm, LSF, PBS, or SGE clusters. The skill generates a reusable launch script configured for multi-backend execution, supporting both local execution and direct scheduler submission for PacBio HiFi somatic analysis.
Launching a PacBio HiFi somatic workflow requires patient and sample identifiers, tumor and normal BAM paths, and exactly one reference mode. The skill validates these inputs, checks indices, and confirms runtime dependencies before generating Nextflow artifacts.
Nextflow supports dry-run validation for pacsomatic pipelines through this skill, which generates a params YAML and launch script to test the configuration. It verifies inputs, indices, and runtime dependencies without executing the full compute workload.
Your pacsomatic Nextflow submission may fail due to missing runtime dependencies or invalid indices. The skill provides troubleshooting support to triage dependency gaps, validate generated artifacts, and offer clear next-step guidance to resolve submission failures.
Estrella-231Generate pacsomatic samplesheets and Nextflow launch artifacts from tumor-normal BAM inputs.
SheshiyerGenerate and schedule pre-launch announcement and reminder emails with JSON handoff.
tassiovaleAutomate creation, execution, and debugging of Nextflow workflows.
Lord1EgyptValidate and execute nf-core/pacsomatic pipelines for tumor-normal BAM analysis.
