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,
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pacsomatic
Overview
This skill provides a reproducible execution workflow for nf-core/pacsomatic, centered on a single helper entrypoint that handles validation, artifact generation, and optional execution.
Primary entrypoint:
scripts/run_pacsomatic.py
The helper script:
validates required identifiers, files, reference mode, and runtime prerequisites
writes a pacsomatic-compatible samplesheet (patient,sample,status,bam,pbi)
generates a params YAML and launch script for repro
[Description truncada. Veja o README completo no GitHub.]
