abi-agent 0.1.0__tar.gz

abi_agent-0.1.0/.gitignore

@@ -0,0 +1,37 @@
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.egg-info/
+dist/
+build/
+*.egg
+
+# Virtual environments
+.venv/
+venv/
+.mamba/
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Project-specific
+results/
+log/
+*.log
+progress.json
+progress.jsonl
+
+# CMake (if used)
+CMakeCache.txt
+CMakeFiles/
+cmake_install.cmake
+Makefile
+CTestTestfile.cmake

abi_agent-0.1.0/CHANGELOG.md

@@ -0,0 +1,27 @@
+# Changelog
+
+## [0.1.0] - 2026-06-12
+
+### Added
+- Initial release as standalone package.
+- Core ABI schemas: `ABISample`, `ABISampleContext`, `ABIPlanStep`, `ABIExecutionPlan`.
+- Plugin system with Python `entry_points` registration.
+- Built-in metatranscriptomics plugin (fastp → STAR → featureCounts).
+- Optional metagenomic_plasmid adapter plugin (requires `autoplasm>=0.1.0`).
+- `GenericABIExecutor` for plan execution with full provenance.
+- `StandardTableManager` for schema-driven TSV table management.
+- DAG inference by path matching for dependency resolution.
+- Local and Nextflow runtime backends.
+- `ABIAgentInterface` for transport-neutral agent integration.
+- OpenAI function calling tool descriptor export.
+- CLI via Typer: `list-types`, `init`, `plan`, `dry-run`, `inspect`, `report`, `run`, `export-nextflow`, `export-openai-tools`.
+- Public SDK entry points for plugin authors: `abi.tools`, `abi.errors`, and `abi.testing`.
+- Plugin contract testing helper (`assert_plugin_contract`).
+- Path-priority dev setup tool (`abi-dev-setup`) for environments where another `abi` package may shadow this one.
+- Runtime warning when `abi` is loaded from an unexpected location.
+
+### Changed
+- CLI and agent planning/execution commands require an explicit ABI analysis type.
+- Metatranscriptomics demo registry uses ABI-owned environment names.
+- Internal compatibility modules no longer define public-facing error classes.
+- Improved type hints and error handling across multiple modules.

abi_agent-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025-2026 ABI Team
+
+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.

abi_agent-0.1.0/PKG-INFO

@@ -0,0 +1,269 @@
+Metadata-Version: 2.4
+Name: abi-agent
+Version: 0.1.0
+Summary: Agent-Bioinformatics Interface: plugin-based abstraction for AI-driven bioinformatics analysis
+Project-URL: Homepage, https://github.com/sleepinlava/abi
+Project-URL: Repository, https://github.com/sleepinlava/abi
+Author-email: BingkangGuo <bingkangguo@gmail.com>
+License-Expression: MIT
+License-File: LICENSE
+Keywords: agent,ai,bioinformatics,metagenomics,pipeline,plasmid
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: rich>=13.0
+Requires-Dist: typer>=0.9
+Provides-Extra: autoplasm
+Requires-Dist: autoplasm>=0.1.0; extra == 'autoplasm'
+Provides-Extra: dev
+Requires-Dist: mypy>=1.0; extra == 'dev'
+Requires-Dist: pytest>=7.0; extra == 'dev'
+Requires-Dist: ruff>=0.4; extra == 'dev'
+Requires-Dist: types-pyyaml>=6.0; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# ABI — Agent-Bioinformatics Interface
+
+A plugin-based Python abstraction layer that lets AI agents drive
+bioinformatics analyses through a unified
+**plan → dry-run → execute → inspect → report** workflow.
+
+[![Python](https://img.shields.io/pypi/pyversions/abi-agent.svg)](https://pypi.org/project/abi-agent/)
+[![PyPI](https://img.shields.io/pypi/v/abi-agent.svg)](https://pypi.org/project/abi-agent/)
+[![License](https://img.shields.io/pypi/l/abi-agent.svg)](https://github.com/sleepinlava/abi/blob/master/LICENSE)
+
+## Installation
+
+```bash
+# From PyPI (core install — metatranscriptomics plugin)
+pip install abi-agent
+
+# Include the optional metagenomic_plasmid adapter
+pip install "abi-agent[autoplasm]"
+
+# Development install (core + all dev tooling)
+pip install "abi-agent[autoplasm,dev]"
+```
+
+**Python**: 3.10 – 3.13
+
+## Quick Start
+
+```bash
+# List installed analysis types
+abi list-types
+
+# Initialize a workspace from a plugin template
+abi init --type metatranscriptomics --outdir ./workspace
+
+# Build an execution plan
+abi plan --type metatranscriptomics --config config.yaml --sample-sheet samples.tsv
+
+# Dry-run — full provenance artifacts, no real tool execution
+abi dry-run --type metatranscriptomics --config config.yaml --sample-sheet samples.tsv
+
+# Execute through a runtime backend
+abi run --type metatranscriptomics --config config.yaml --sample-sheet samples.tsv
+
+# Inspect results
+abi inspect --result-dir results/
+
+# Regenerate reports
+abi report --result-dir results/ --type metatranscriptomics
+
+# Export to Nextflow DSL2
+abi export-nextflow --type metatranscriptomics --output workflow.nf
+
+# Export OpenAI-compatible tool descriptors
+abi export-openai-tools --type metatranscriptomics --format responses
+```
+
+All commands support `--output-json` for structured agent consumption.
+
+## Optional Dependencies
+
+| Extra        | Plugin                | Package    | Install                                |
+|-------------|-----------------------|------------|----------------------------------------|
+| `autoplasm` | `metagenomic_plasmid` | autoplasm  | `pip install abi-agent[autoplasm]`     |
+| `dev`       | (development tooling) | pytest, ruff, mypy, types-PyYAML | `pip install abi-agent[dev]` |
+
+The `metagenomic_plasmid` plugin uses **lazy imports** — the external package is
+imported inside each method, not at the module top level. The plugin module
+loads without its dependency; a clear `ImportError` is raised only when you
+actually try to use it.
+
+## Architecture
+
+```
+CLI (Typer)  ────  ABIAgentInterface  ────  OpenAI Tool Export
+ │                    │
+ └── Plugin Registry (entry_points + builtins)
+       │
+       └── Plugin Protocol ───────────────────────────────────────┐
+            ├── ABIPlugin           (6 core methods)              │
+            ├── ABIDryRunPlugin     (+ execute_dry_run)           │
+            └── ABIInitializablePlugin  (+ root path for init)    │
+                     │                                            │
+                     └── Runtime Backend (Local / Nextflow)       │
+                              │                                   │
+                              └── GenericABIExecutor              │
+                                   ├── Standard Tables (TSV)      │
+                                   ├── Provenance (JSON / JSONL)  │
+                                   └── Reports (Markdown / HTML)  │
+                                                                    │
+Public SDK for plugin authors:  abi.tools  abi.errors  abi.testing ◄┘
+```
+
+## Plugin Development
+
+A plugin is any object that satisfies the `ABIPlugin` protocol. It must expose
+four string attributes and six methods:
+
+```python
+from abi.interfaces import ABIPlugin
+from abi.schemas import ABIExecutionPlan
+from abi.tools import ToolRegistry
+
+
+class MyPlugin:
+    # ── attributes ──────────────────────────────────────────────
+    plugin_id: str
+    display_name: str
+    description: str
+    report_title: str
+
+    # ── 6 core methods ──────────────────────────────────────────
+    def load_config(self, config_path, *, profile, overrides) -> dict: ...
+    def build_plan(self, config, *, check_files) -> ABIExecutionPlan: ...
+    def registry(self) -> ToolRegistry: ...
+    def table_schemas(self) -> dict[str, list[str]]: ...
+    def parse_outputs(self, tool_id, output_dir, sample_id) -> dict: ...
+    def write_report(self, plan, result_dir) -> dict: ...
+```
+
+### Extended Protocols
+
+**`ABIDryRunPlugin`** — add `execute_dry_run` to use a plugin-specific
+dry-run pipeline instead of the generic executor:
+
+```python
+from abi.interfaces import ABIDryRunPlugin
+
+class MyPlugin(ABIDryRunPlugin):
+    def execute_dry_run(self, plan, config) -> dict[str, Path]: ...
+```
+
+**`ABIInitializablePlugin`** — expose a `root` path so `abi init` can copy
+template files (config, sample sheet) into a workspace:
+
+```python
+from abi.interfaces import ABIInitializablePlugin
+
+class MyPlugin(ABIInitializablePlugin):
+    root: Path  # directory containing config_default.yaml and sample_sheet_template.tsv
+```
+
+### Registration
+
+Register via `pyproject.toml` entry points:
+
+```toml
+[project.entry-points."abi.plugins"]
+my_analysis = "my_package.plugins:MyPlugin"
+```
+
+### Testing
+
+Validate a plugin's contract with the SDK testing helper:
+
+```python
+from abi.plugins import get_plugin
+from abi.testing import assert_plugin_contract
+
+
+def test_my_plugin_contract():
+    assert_plugin_contract(get_plugin("my_analysis"))
+```
+
+## SDK Reference
+
+Public modules available to plugin authors:
+
+| Module             | Contents                                              |
+|-------------------|-------------------------------------------------------|
+| `abi.tools`       | `ToolRegistry`, `ToolSkill`, `RunResult`             |
+| `abi.errors`      | `ABIError`, `ConfigError`, `SampleSheetError`, `ToolError` |
+| `abi.testing`     | `assert_plugin_contract`                              |
+| `abi.schemas`     | `ABISample`, `ABISampleContext`, `ABIPlanStep`, `ABIExecutionPlan` |
+| `abi.interfaces`  | `ABIPlugin`, `ABIDryRunPlugin`, `ABIInitializablePlugin` |
+
+## Development
+
+```bash
+# Editable install with dev tooling
+pip install -e ".[dev]"
+
+# Lint, type-check, and test
+ruff check src/ && ruff format --check src/ tests/
+mypy src/abi/ --ignore-missing-imports
+pytest tests/ -v
+
+# Build distribution
+pip install build twine
+python -m build
+python -m twine check dist/*
+```
+
+The test suite does **not** require `autoplasm` — CI installs only `.[dev]`.
+
+## Publishing to PyPI
+
+The package is configured for PyPI publication as `abi-agent`. Built-in plugin
+templates under `plugins/` are included in both source distributions and wheels
+so `abi init` works after installation from PyPI.
+
+Preferred release path:
+
+1. Ensure `pyproject.toml` has the intended version.
+2. Create and publish a GitHub Release for that version.
+3. The `Publish to PyPI` workflow builds the source distribution and wheel,
+   validates them with `twine check`, and publishes via PyPI Trusted Publishing.
+
+Manual release path, if you have a PyPI API token:
+
+```bash
+rm -rf dist/
+python -m build
+python -m twine check dist/*
+python -m twine upload dist/*
+```
+
+Set `TWINE_USERNAME=__token__` and `TWINE_PASSWORD=<pypi-api-token>` for manual
+uploads.
+
+### Path Conflict with PlasimSkillsForAgent
+
+If you also have the `autoplasm` package installed from the
+PlasimSkillsForAgent monorepo, its `abi` package can shadow the standalone
+`abi-agent` package on `sys.path`.  Run the dev-setup tool once to fix this:
+
+```bash
+abi-dev-setup                          # install priority .pth file
+abi-dev-setup --check                  # verify the fix is active
+abi-dev-setup --undo                   # remove the fix
+```
+
+When the wrong package is loaded at runtime, a warning is emitted with
+instructions.  The CI pipeline is unaffected (clean environment).
+
+## License
+
+MIT — see [LICENSE](LICENSE).

abi_agent-0.1.0/README.md

@@ -0,0 +1,237 @@
+# ABI — Agent-Bioinformatics Interface
+
+A plugin-based Python abstraction layer that lets AI agents drive
+bioinformatics analyses through a unified
+**plan → dry-run → execute → inspect → report** workflow.
+
+[![Python](https://img.shields.io/pypi/pyversions/abi-agent.svg)](https://pypi.org/project/abi-agent/)
+[![PyPI](https://img.shields.io/pypi/v/abi-agent.svg)](https://pypi.org/project/abi-agent/)
+[![License](https://img.shields.io/pypi/l/abi-agent.svg)](https://github.com/sleepinlava/abi/blob/master/LICENSE)
+
+## Installation
+
+```bash
+# From PyPI (core install — metatranscriptomics plugin)
+pip install abi-agent
+
+# Include the optional metagenomic_plasmid adapter
+pip install "abi-agent[autoplasm]"
+
+# Development install (core + all dev tooling)
+pip install "abi-agent[autoplasm,dev]"
+```
+
+**Python**: 3.10 – 3.13
+
+## Quick Start
+
+```bash
+# List installed analysis types
+abi list-types
+
+# Initialize a workspace from a plugin template
+abi init --type metatranscriptomics --outdir ./workspace
+
+# Build an execution plan
+abi plan --type metatranscriptomics --config config.yaml --sample-sheet samples.tsv
+
+# Dry-run — full provenance artifacts, no real tool execution
+abi dry-run --type metatranscriptomics --config config.yaml --sample-sheet samples.tsv
+
+# Execute through a runtime backend
+abi run --type metatranscriptomics --config config.yaml --sample-sheet samples.tsv
+
+# Inspect results
+abi inspect --result-dir results/
+
+# Regenerate reports
+abi report --result-dir results/ --type metatranscriptomics
+
+# Export to Nextflow DSL2
+abi export-nextflow --type metatranscriptomics --output workflow.nf
+
+# Export OpenAI-compatible tool descriptors
+abi export-openai-tools --type metatranscriptomics --format responses
+```
+
+All commands support `--output-json` for structured agent consumption.
+
+## Optional Dependencies
+
+| Extra        | Plugin                | Package    | Install                                |
+|-------------|-----------------------|------------|----------------------------------------|
+| `autoplasm` | `metagenomic_plasmid` | autoplasm  | `pip install abi-agent[autoplasm]`     |
+| `dev`       | (development tooling) | pytest, ruff, mypy, types-PyYAML | `pip install abi-agent[dev]` |
+
+The `metagenomic_plasmid` plugin uses **lazy imports** — the external package is
+imported inside each method, not at the module top level. The plugin module
+loads without its dependency; a clear `ImportError` is raised only when you
+actually try to use it.
+
+## Architecture
+
+```
+CLI (Typer)  ────  ABIAgentInterface  ────  OpenAI Tool Export
+ │                    │
+ └── Plugin Registry (entry_points + builtins)
+       │
+       └── Plugin Protocol ───────────────────────────────────────┐
+            ├── ABIPlugin           (6 core methods)              │
+            ├── ABIDryRunPlugin     (+ execute_dry_run)           │
+            └── ABIInitializablePlugin  (+ root path for init)    │
+                     │                                            │
+                     └── Runtime Backend (Local / Nextflow)       │
+                              │                                   │
+                              └── GenericABIExecutor              │
+                                   ├── Standard Tables (TSV)      │
+                                   ├── Provenance (JSON / JSONL)  │
+                                   └── Reports (Markdown / HTML)  │
+                                                                    │
+Public SDK for plugin authors:  abi.tools  abi.errors  abi.testing ◄┘
+```
+
+## Plugin Development
+
+A plugin is any object that satisfies the `ABIPlugin` protocol. It must expose
+four string attributes and six methods:
+
+```python
+from abi.interfaces import ABIPlugin
+from abi.schemas import ABIExecutionPlan
+from abi.tools import ToolRegistry
+
+
+class MyPlugin:
+    # ── attributes ──────────────────────────────────────────────
+    plugin_id: str
+    display_name: str
+    description: str
+    report_title: str
+
+    # ── 6 core methods ──────────────────────────────────────────
+    def load_config(self, config_path, *, profile, overrides) -> dict: ...
+    def build_plan(self, config, *, check_files) -> ABIExecutionPlan: ...
+    def registry(self) -> ToolRegistry: ...
+    def table_schemas(self) -> dict[str, list[str]]: ...
+    def parse_outputs(self, tool_id, output_dir, sample_id) -> dict: ...
+    def write_report(self, plan, result_dir) -> dict: ...
+```
+
+### Extended Protocols
+
+**`ABIDryRunPlugin`** — add `execute_dry_run` to use a plugin-specific
+dry-run pipeline instead of the generic executor:
+
+```python
+from abi.interfaces import ABIDryRunPlugin
+
+class MyPlugin(ABIDryRunPlugin):
+    def execute_dry_run(self, plan, config) -> dict[str, Path]: ...
+```
+
+**`ABIInitializablePlugin`** — expose a `root` path so `abi init` can copy
+template files (config, sample sheet) into a workspace:
+
+```python
+from abi.interfaces import ABIInitializablePlugin
+
+class MyPlugin(ABIInitializablePlugin):
+    root: Path  # directory containing config_default.yaml and sample_sheet_template.tsv
+```
+
+### Registration
+
+Register via `pyproject.toml` entry points:
+
+```toml
+[project.entry-points."abi.plugins"]
+my_analysis = "my_package.plugins:MyPlugin"
+```
+
+### Testing
+
+Validate a plugin's contract with the SDK testing helper:
+
+```python
+from abi.plugins import get_plugin
+from abi.testing import assert_plugin_contract
+
+
+def test_my_plugin_contract():
+    assert_plugin_contract(get_plugin("my_analysis"))
+```
+
+## SDK Reference
+
+Public modules available to plugin authors:
+
+| Module             | Contents                                              |
+|-------------------|-------------------------------------------------------|
+| `abi.tools`       | `ToolRegistry`, `ToolSkill`, `RunResult`             |
+| `abi.errors`      | `ABIError`, `ConfigError`, `SampleSheetError`, `ToolError` |
+| `abi.testing`     | `assert_plugin_contract`                              |
+| `abi.schemas`     | `ABISample`, `ABISampleContext`, `ABIPlanStep`, `ABIExecutionPlan` |
+| `abi.interfaces`  | `ABIPlugin`, `ABIDryRunPlugin`, `ABIInitializablePlugin` |
+
+## Development
+
+```bash
+# Editable install with dev tooling
+pip install -e ".[dev]"
+
+# Lint, type-check, and test
+ruff check src/ && ruff format --check src/ tests/
+mypy src/abi/ --ignore-missing-imports
+pytest tests/ -v
+
+# Build distribution
+pip install build twine
+python -m build
+python -m twine check dist/*
+```
+
+The test suite does **not** require `autoplasm` — CI installs only `.[dev]`.
+
+## Publishing to PyPI
+
+The package is configured for PyPI publication as `abi-agent`. Built-in plugin
+templates under `plugins/` are included in both source distributions and wheels
+so `abi init` works after installation from PyPI.
+
+Preferred release path:
+
+1. Ensure `pyproject.toml` has the intended version.
+2. Create and publish a GitHub Release for that version.
+3. The `Publish to PyPI` workflow builds the source distribution and wheel,
+   validates them with `twine check`, and publishes via PyPI Trusted Publishing.
+
+Manual release path, if you have a PyPI API token:
+
+```bash
+rm -rf dist/
+python -m build
+python -m twine check dist/*
+python -m twine upload dist/*
+```
+
+Set `TWINE_USERNAME=__token__` and `TWINE_PASSWORD=<pypi-api-token>` for manual
+uploads.
+
+### Path Conflict with PlasimSkillsForAgent
+
+If you also have the `autoplasm` package installed from the
+PlasimSkillsForAgent monorepo, its `abi` package can shadow the standalone
+`abi-agent` package on `sys.path`.  Run the dev-setup tool once to fix this:
+
+```bash
+abi-dev-setup                          # install priority .pth file
+abi-dev-setup --check                  # verify the fix is active
+abi-dev-setup --undo                   # remove the fix
+```
+
+When the wrong package is loaded at runtime, a warning is emitted with
+instructions.  The CI pipeline is unaffected (clean environment).
+
+## License
+
+MIT — see [LICENSE](LICENSE).

abi_agent-0.1.0/examples/fixtures/tiny_R1.fastq

@@ -0,0 +1,8 @@
+@read1
+ACGTCGACGT
++
+IIIIIIIIII
+@read2
+GTCGACGTCG
++
+IIIIIIIIII

abi_agent-0.1.0/examples/fixtures/tiny_R2.fastq

@@ -0,0 +1,8 @@
+@read1
+CGTACGTACG
++
+IIIIIIIIII
+@read2
+TACGATCGAT
++
+IIIIIIIIII

abi_agent-0.1.0/examples/sample_sheet_transcriptomics.tsv

@@ -0,0 +1,2 @@
+sample_id	condition	read1	read2
+RNA1	control	examples/fixtures/tiny_R1.fastq	examples/fixtures/tiny_R2.fastq

abi_agent-0.1.0/plugins/metagenomic_plasmid/README.md

@@ -0,0 +1,12 @@
+# Metagenomic Plasmid Plugin
+
+This plugin is an adapter over the existing AutoPlasm implementation.
+
+It requires the `autoplasm` package to be installed:
+
+```bash
+pip install abi-agent[autoplasm]
+```
+
+When installed, it delegates planning, execution, parsing, and reporting to AutoPlasm's
+planner, pipeline executor, parsers, and report generators.

abi_agent-0.1.0/plugins/metatranscriptomics/config_default.yaml

@@ -0,0 +1,21 @@
+project_name: abi_metatranscriptomics_demo
+analysis_type: metatranscriptomics
+mode: auto
+threads: 4
+outdir: results/abi_metatranscriptomics_demo
+log_dir: log
+dry_run: false
+mock_tools: false
+
+execution:
+  progress: true
+
+input:
+  sample_sheet: examples/sample_sheet_transcriptomics.tsv
+
+alignment:
+  tool: star
+
+resources:
+  genome_index: GENOME_INDEX_NOT_CONFIGURED
+  annotation_gtf: ANNOTATION_GTF_NOT_CONFIGURED

abi_agent-0.1.0/plugins/metatranscriptomics/sample_sheet_template.tsv

@@ -0,0 +1,2 @@
+sample_id	condition	read1	read2
+RNA1	control	examples/fixtures/tiny_R1.fastq	examples/fixtures/tiny_R2.fastq

abi_agent-0.1.0/plugins/metatranscriptomics/skills/fastp/SKILL.md

@@ -0,0 +1,33 @@
+# fastp
+
+## Purpose
+Trim and quality-control paired-end RNA-seq reads before alignment.
+
+## When to Use
+Use for the metatranscriptomics demo `qc` step when paired FASTQ inputs are present.
+
+## Inputs
+- `read1`
+- `read2`
+- `sample_id`
+- `output_dir`
+- `threads`
+
+## Outputs
+- Cleaned paired FASTQ files under `01_qc/{sample_id}/`.
+- HTML and JSON QC summaries.
+- ABI provenance records in `provenance/commands.tsv` and `provenance/step_logs/`.
+
+## Environment
+Runs from the repository-local `abi-qc` environment as `fastp`.
+
+## Command Template
+```bash
+fastp -i {read1} -I {read2} -o {output_dir}/{sample_id}_R1.clean.fastq.gz -O {output_dir}/{sample_id}_R2.clean.fastq.gz --thread {threads} --html {output_dir}/{sample_id}.fastp.html --json {output_dir}/{sample_id}.fastp.json
+```
+
+## Failure Handling
+Check input FASTQ paths, the `abi-qc` environment, and the per-step stderr log.
+
+## Normalization
+Future real-run parsers can append read metrics to `qc_summary.tsv`.