Pacsomatic

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 reproducible reruns
• supports dry-run validation and run/submit execution paths

Use this skill as the default path for pacsomatic operations. Do not bypass it with manually assembled nextflow run nf-core/pacsomatic commands unless the user explicitly asks for manual command construction.

When to Use This Skill

Invoke this skill when the user asks to:

• run matched tumor-normal analysis from BAM files
• generate or fix pacsomatic samplesheet and launch artifacts
• execute locally or submit to schedulers (LSF/Slurm/PBS/SGE)
• perform dry-run validation before execution
• troubleshoot launch failures or summarize run outputs

Do not use this skill for:

• deep biological interpretation beyond run-level sanity checks
• editing pipeline internals unless explicitly requested

Typical trigger phrases:

• "run nf-core/pacsomatic for this tumor-normal pair"
• "prepare pacsomatic samplesheet and launch script"
• "do a dry run first and tell me what is missing"
• "submit pacsomatic to slurm/lsf and return the job id"
• "why did pacsomatic submission fail"

Routing and Execution Rules

• Always collect required run inputs first.
• Always route through scripts/run_pacsomatic.py for validation and artifact generation.
• Default to --dry-run when the user asks for checks/validation only.
• Use --run only when the user asks to execute/submit.
• For scheduler modes, include executor-specific resource arguments and return detected job ID when available.
• If execution fails, report first failure point and next triage target (.nextflow.log, pipeline_info, failing task logs).

Inputs Required

Required:

• tumor BAM path
• normal BAM path
• patient ID
• tumor sample ID
• normal sample ID
• output directory
• exactly one reference mode: --fasta or --genome

Optional:

• profile, resources, scheduler account/queue
• pipeline version (-r)
• params file, resume/report/dag flags
• --dry-run and/or --run

Workflow

• Validate identity and input constraints.
• Validate required local paths (BAM, optional PBI, optional FASTA).
• Resolve runtime and dependency checks.
• Build samplesheet and generated params YAML.
• Generate launch script for selected executor.
• If --dry-run and not --run, stop after artifact generation.
• If --run, execute locally or submit to scheduler.
• Return command/script path, validation status, and job ID (if detected).

Agent Response Contract

Every response after invocation should include:

• exact command used or generated script path
• confirmation that validation checks ran
• run type (dry-run vs run)
• scheduler job ID when available
• one concrete next step for validation/triage

Quick Start

Dry run:

python scripts/run_pacsomatic.py \
  --tumor-bam /path/to/tumor.bam \
  --normal-bam /path/to/normal.bam \
  --patient-id P001 \
  --tumor-sample-id P001_T \
  --normal-sample-id P001_N \
  --outdir /path/to/output \
  --genome GRCh38 \
  --profile singularity,sanger \
  --dry-run

Scheduler execution example (Slurm):

python scripts/run_pacsomatic.py \
  --tumor-bam /path/to/tumor.bam \
  --normal-bam /path/to/normal.bam \
  --patient-id P001 \
  --tumor-sample-id P001_T \
  --normal-sample-id P001_N \
  --outdir /path/to/output \
  --genome GRCh38 \
  --profile singularity,sanger \
  --executor slurm \
  --queue compute \
  --project my_account \
  --cpus 16 \
  --memory-gb 64 \
  --walltime 48:00 \
  --run

Configuration

Use config.yaml as the baseline for profile/executor/runtime defaults. Override at invocation time when user requirements differ.

Testing

Run unit tests from skill root:

python -m unittest discover -s tests/pacsomatic -v

References

• references/agent-playbook.md
• references/config-and-output.md
• references/pacsomatic_guide.md
• scripts/run_pacsomatic.py