What problem does it solve?
It solves the problem of reliably preparing matched tumor-normal PacBio HiFi runs by validating BAM/reference inputs, generating a correct pacsomatic samplesheet, and producing reproducible Nextflow launch artifacts for local or scheduler execution.
Core Features & Use Cases
- Samplesheet generation: Creates a pacsomatic-compatible samplesheet with required columns (patient,sample,status,bam,pbi).
- Reproducible launch artifact creation: Writes a generated params YAML plus an executor-specific launch script so reruns are consistent.
- Pre-flight validation and troubleshooting: Performs input/path checks, validates identifiers (no spaces), verifies runtime/tool availability (e.g., Nextflow/Java/container tooling), and returns actionable failure points.
- Dry-run then execute/submit workflow: Supports generate-only and dry-run validation, then optional execution/submission using local, LSF, Slurm, PBS, or SGE.
- Use case: You have one tumor BAM and one normal BAM for a patient and need to validate inputs, generate the correct artifacts, and then submit a scheduler job without manually crafting Nextflow commands.
Quick Start
Run a dry-run validation and generate the pacsomatic samplesheet and launch assets for your tumor-normal BAM pair by calling the helper script with your BAM paths, IDs, output directory, and either --genome GRCh38 or --fasta /path/to/reference.fa.
