feat: add pacsomatic skill

scientific-skills/pacsomatic/LICENSE

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+MIT License
+
+Copyright (c) 2026 Beifang Niu
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

scientific-skills/pacsomatic/README.md

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+# pacsomatic skill
+
+This directory packages the nf-core/pacsomatic operator skill.
+
+## Layout
+
+- `SKILL.md`: skill contract and usage guidance
+- `config.yaml`: baseline defaults for runtime/execution/validation behavior
+- `references/`: operator guidance and troubleshooting notes
+- `scripts/run_pacsomatic.py`: execution helper
+- `tests/`: unit tests for helper behavior
+
+## Run tests
+
+```bash
+cd pacsomatic
+python -m unittest discover -s tests -v
+```

scientific-skills/pacsomatic/SKILL.md

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+---
+name: pacsomatic
+description: 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.
+license: MIT
+metadata:
+    skill-author: Beifang Niu
+    contributors:
+      - Haidong
+      - Wenchao
+    upstream-pipeline: https://github.com/nf-core/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
+
+1. Always collect required run inputs first.
+2. Always route through `scripts/run_pacsomatic.py` for validation and artifact generation.
+3. Default to `--dry-run` when the user asks for checks/validation only.
+4. Use `--run` only when the user asks to execute/submit.
+5. For scheduler modes, include executor-specific resource arguments and return detected job ID when available.
+6. 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
+
+1. Validate identity and input constraints.
+2. Validate required local paths (BAM, optional PBI, optional FASTA).
+3. Resolve runtime and dependency checks.
+4. Build samplesheet and generated params YAML.
+5. Generate launch script for selected executor.
+6. If `--dry-run` and not `--run`, stop after artifact generation.
+7. If `--run`, execute locally or submit to scheduler.
+8. 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:
+
+```bash
+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):
+
+```bash
+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:
+
+```bash
+python -m unittest discover -s tests -v
+```
+
+## References
+
+- `references/agent-playbook.md`
+- `references/config-and-output.md`
+- `references/pacsomatic_guide.md`
+- `scripts/run_pacsomatic.py`

scientific-skills/pacsomatic/config.yaml

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+# Baseline configuration for nf-core/pacsomatic skill usage.
+# These values are intended as defaults for operators and agents.
+
+pipeline:
+  name: nf-core/pacsomatic
+  repo_url: https://github.com/nf-core/pacsomatic.git
+  default_version: ""
+
+runtime:
+  conda_env: pacsomatic-nextflow
+  use_current_path: false
+  create_conda_env: false
+  conda_env_file: ""
+
+execution:
+  profile: singularity,sanger
+  executor: local  # local | none | lsf | slurm | pbs | sge
+  cpus: 16
+  memory_gb: 64
+  walltime: "48:00"
+  queue: ""
+  project: ""
+  job_name: pacsomatic
+
+outputs:
+  samplesheet_name: samplesheet.csv
+  generated_params_name: pacsomatic.params.generated.yaml
+  launch_script_suffix_local: local
+  default_workdir_name: work
+
+validation:
+  enforce_no_spaces_in_ids: true
+  require_exactly_one_reference_mode: true
+  warn_if_bam_index_missing: true
+  min_java_major: 17
+
+agent_response:
+  include_command_or_script_path: true
+  include_validation_confirmation: true
+  include_run_type: true
+  include_job_id_if_available: true
+  include_next_triage_step: true

scientific-skills/pacsomatic/references/agent-playbook.md

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+# Agent Playbook
+
+## What The User Needs To Provide
+
+Users only need to provide run inputs; they do not need to know pipeline internals:
+
+- tumor BAM path
+- normal BAM path
+- reference input (`--fasta` path or `--genome` key)
+- output directory
+
+Optional:
+
+- sample metadata IDs
+- executor/resource preferences
+- optional `pbi` paths
+
+No repository checkout directory is required for this skill.
+
+Use this sequence when helping a user run nf-core/pacsomatic:
+
+1. Collect required inputs.
+   - tumor BAM
+   - normal BAM
+   - patient ID
+   - tumor sample ID
+   - normal sample ID
+   - output directory
+   - one reference mode: `--fasta` or `--genome`
+2. Validate naming rules.
+   Patient/sample identifiers cannot contain spaces.
+3. Validate local input paths.
+   Local BAMs must exist. `pbi` is optional, but if provided the file must exist.
+4. Start with a dry run when uncertain.
+   Use `--dry-run` to validate assumptions and generate artifacts without scheduling.
+5. Launch when requested.
+   Use `--run` with a selected `--executor` (`local`, `lsf`, `slurm`, `pbs`, or `sge`).
+6. After submission.
+   Report generated samplesheet path, script path, printed run command, and detected job ID if present.
+7. If pipeline fails later.
+   Inspect launcher logs first, then Nextflow report and DAG outputs.
+
+Recommended helper command:
+
+```bash
+python .github/skills/pacsomatic/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 local \
+  --dry-run
+```
+
+Launch command variant:
+
+```bash
+python .github/skills/pacsomatic/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 \
+  --fasta /path/to/reference.fa \
+  --profile singularity,sanger \
+   --executor lsf \
+  --run
+```