{"page":{"pageid":520,"slug":"skill-scientific-pacsomatic","title":"pacsomatic skill (K-Dense scientific-agent-skills)","content":"**What it does.** 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, perform dry-run checks, or troubleshoot pipeline startup and scheduler submission errors. Part of [[skills-scientific-agent-skills]] (K-Dense-AI/scientific-agent-skills).\n\n| | |\n| --- | --- |\n| Upstream | [K-Dense-AI/scientific-agent-skills](https://github.com/K-Dense-AI/scientific-agent-skills) |\n| Skill file | [skills/pacsomatic/SKILL.md](https://github.com/K-Dense-AI/scientific-agent-skills/blob/HEAD/skills/pacsomatic/SKILL.md) |\n| License | MIT (skill folder LICENSE) |\n| Author | K-Dense Inc. |\n| Fetched | 2026-09-10 |\n\n## Install\n\n- `npx skills add K-Dense-AI/scientific-agent-skills --skill pacsomatic`, or copy the skill folder into `~/.claude/skills/pacsomatic/`.\n- Raw file: `curl -sL https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/pacsomatic/SKILL.md`\n\n## SKILL.md (verbatim)\n\n```yaml\nname: pacsomatic\ndescription: 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, perform dry-run checks, or troubleshoot pipeline startup and scheduler submission errors.\nlicense: MIT\nmetadata:\n version: \"1.2\"\n skill-author: Beifang Niu\n contributors: Haidong, Wenchao\n upstream-pipeline: https://github.com/nf-core/pacsomatic\n```\n\n# pacsomatic\n\n## Overview\n\nThis skill provides a reproducible execution workflow for nf-core/pacsomatic, centered on a single helper entrypoint that handles validation, artifact generation, and optional execution.\n\nPrimary entrypoint:\n- `scripts/run_pacsomatic.py`\n\nThe helper script:\n- validates required identifiers, files, reference mode, and runtime prerequisites\n- writes a pacsomatic-compatible samplesheet (`patient,sample,status,bam,pbi`)\n- generates a params YAML and launch script for reproducible reruns\n- supports dry-run validation and run/submit execution paths\n\nUse 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.\n\n## When to Use This Skill\n\nInvoke this skill when the user asks to:\n- run matched tumor-normal analysis from BAM files\n- generate or fix pacsomatic samplesheet and launch artifacts\n- execute locally or submit to schedulers (LSF/Slurm/PBS/SGE)\n- perform dry-run validation before execution\n- troubleshoot launch failures or summarize run outputs\n\nDo not use this skill for:\n- deep biological interpretation beyond run-level sanity checks\n- editing pipeline internals unless explicitly requested\n\nTypical trigger phrases:\n- \"run nf-core/pacsomatic for this tumor-normal pair\"\n- \"prepare pacsomatic samplesheet and launch script\"\n- \"do a dry run first and tell me what is missing\"\n- \"submit pacsomatic to slurm/lsf and return the job id\"\n- \"why did pacsomatic submission fail\"\n\n## Routing and Execution Rules\n\n1. Always collect required run inputs first.\n2. Always route through `scripts/run_pacsomatic.py` for validation and artifact generation.\n3. Default to `--dry-run` when the user asks for checks/validation only.\n4. Use `--run` only when the user asks to execute/submit.\n5. For scheduler modes, include executor-specific resource arguments and return detected job ID when available.\n6. If execution fails, report first failure point and next triage target (`.nextflow.log`, `pipeline_info`, failing task logs).\n\n## Inputs Required\n\nRequired:\n- tumor BAM path\n- normal BAM path\n- patient ID\n- tumor sample ID\n- normal sample ID\n- output directory\n- exactly one reference mode: `--fasta` or `--genome`\n\nOptional:\n- profile, resources, scheduler account/queue\n- pipeline version (`-r`)\n- params file, resume/report/dag flags\n- `--dry-run` and/or `--run`\n\n## Workflow\n\n1. Validate identity and input constraints.\n2. Validate required local paths (BAM, optional PBI, optional FASTA).\n3. Resolve runtime and dependency checks.\n4. Build samplesheet and generated params YAML.\n5. Generate launch script for selected executor.\n6. If `--dry-run` and not `--run`, stop after artifact generation.\n7. If `--run`, execute locally or submit to scheduler.\n8. Return command/script path, validation status, and job ID (if detected).\n\n## Agent Response Contract\n\nEvery response after invocation should include:\n- exact command used or generated script path\n- confirmation that validation checks ran\n- run type (`dry-run` vs `run`)\n- scheduler job ID when available\n- one concrete next step for validation/triage\n\n## Quick Start\n\nDry run:\n\n```bash\npython scripts/run_pacsomatic.py \\\n --tumor-bam /path/to/tumor.bam \\\n --normal-bam /path/to/normal.bam \\\n --patient-id P001 \\\n --tumor-sample-id P001_T \\\n --normal-sample-id P001_N \\\n --outdir /path/to/output \\\n --genome GRCh38 \\\n --profile singularity,sanger \\\n --dry-run\n```\n\nScheduler execution example (Slurm):\n\n```bash\npython scripts/run_pacsomatic.py \\\n --tumor-bam /path/to/tumor.bam \\\n --normal-bam /path/to/normal.bam \\\n --patient-id P001 \\\n --tumor-sample-id P001_T \\\n --normal-sample-id P001_N \\\n --outdir /path/to/output \\\n --genome GRCh38 \\\n --profile singularity,sanger \\\n --executor slurm \\\n --queue compute \\\n --project my_account \\\n --cpus 16 \\\n --memory-gb 64 \\\n --walltime 48:00 \\\n --run\n```\n\n## Configuration\n\nUse `config.yaml` as the baseline for profile/executor/runtime defaults. Override at invocation time when user requirements differ.\n\n## Testing\n\nRun unit tests from skill root:\n\n```bash\npython -m unittest discover -s tests/pacsomatic -v\n```\n\n## References\n\n- `references/agent-playbook.md`\n- `references/config-and-output.md`\n- `references/pacsomatic_guide.md`\n- `scripts/run_pacsomatic.py`\n\n## Other files in this skill\n\n- [LICENSE](https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/pacsomatic/LICENSE)\n- [config.yaml](https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/pacsomatic/config.yaml)\n- [references/agent-playbook.md](https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/pacsomatic/references/agent-playbook.md)\n- [references/config-and-output.md](https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/pacsomatic/references/config-and-output.md)\n- [references/pacsomatic_guide.md](https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/pacsomatic/references/pacsomatic_guide.md)\n- [scripts/run_pacsomatic.py](https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/pacsomatic/scripts/run_pacsomatic.py)\n\n## references/agent-playbook.md (verbatim)\n\n# Agent Playbook\n\n## What The User Needs To Provide\n\nUsers only need to provide run inputs; they do not need to know pipeline internals:\n\n- tumor BAM path\n- normal BAM path\n- reference input (`--fasta` path or `--genome` key)\n- output directory\n\nOptional:\n\n- sample metadata IDs\n- executor/resource preferences\n- optional `pbi` paths\n\nNo repository checkout directory is required for this skill.\n\nUse this sequence when helping a user run nf-core/pacsomatic:\n\n1. Collect required inputs.\n - tumor BAM\n - normal BAM\n - patient ID\n - tumor sample ID\n - normal sample ID\n - output directory\n - one reference mode: `--fasta` or `--genome`\n2. Validate naming rules.\n Patient/sample identifiers cannot contain spaces.\n3. Validate local input paths.\n Local BAMs must exist. `pbi` is optional, but if provided the file must exist.\n4. Start with a dry run when uncertain.\n Use `--dry-run` to validate assumptions and generate artifacts without scheduling.\n5. Launch when requested.\n Use `--run` with a selected `--executor` (`local`, `lsf`, `slurm`, `pbs`, or `sge`).\n6. After submission.\n Report generated samplesheet path, script path, printed run command, and detected job ID if present.\n7. If pipeline fails later.\n Inspect launcher logs first, then Nextflow report and DAG outputs.\n\nRecommended helper command:\n\n```bash\npython .github/skills/pacsomatic/scripts/run_pacsomatic.py \\\n --tumor-bam /path/to/tumor.bam \\\n --normal-bam /path/to/normal.bam \\\n --patient-id P001 \\\n --tumor-sample-id P001_T \\\n --normal-sample-id P001_N \\\n --outdir /path/to/output \\\n --genome GRCh38 \\\n --profile singularity,sanger \\\n --executor local \\\n --dry-run\n```\n\nLaunch command variant:\n\n```bash\npython .github/skills/pacsomatic/scripts/run_pacsomatic.py \\\n --tumor-bam /path/to/tumor.bam \\\n --normal-bam /path/to/normal.bam \\\n --patient-id P001 \\\n --tumor-sample-id P001_T \\\n --normal-sample-id P001_N \\\n --outdir /path/to/output \\\n --fasta /path/to/reference.fa \\\n --profile singularity,sanger \\\n --executor lsf \\\n --run\n```\n\n## references/config-and-output.md (verbatim)\n\n# Config And Output\n\n## Required Inputs\n\n- `--tumor-bam`: tumor BAM path\n- `--normal-bam`: normal BAM path\n- `--patient-id`\n- `--tumor-sample-id`\n- `--normal-sample-id`\n- `--outdir`\n- one reference mode:\n - `--fasta`, or\n - `--genome`\n\n## Core Optional Controls\n\n- `--profile`: Nextflow profile list (for example `singularity,sanger`)\n- `--pipeline-version`: release pin for reproducibility\n- `--params-file`: structured pipeline params\n- `--resume`: rerun interrupted work\n- `--with-report`: Nextflow report path\n- `--with-dag`: Nextflow DAG path\n\n## Execution Backend Controls\n\n- `--executor`: `local`, `none`, `lsf`, `slurm`, `pbs`, or `sge`\n\nDirect CLI execution is supported in all modes. When `--run` is used, the\nhelper runs backend-native launch commands:\n\n- `local` / `none`: `bash