fix(lint): satisfy pre-commit formatting

cursoragent · FloWuenne · cursoragent · commit 4aceb4aa7a75 · 2026-04-20T18:48:48.000Z
Co-authored-by: Florian Wuennemann &lt;flowuenne@gmail.com&gt;
diff --git a/.seqera/context/ERRORS.md b/.seqera/context/ERRORS.md
@@ -61,4 +61,3 @@ Both runs `1cF65l2PDvxNd5` (maniac_celsius) and `5VGC0gjEmghOaz` (clever_kalman)
 - **No failed runs analysed:** Both Platform runs are currently successful. To populate this section with real failure analysis, re-run context generation after a failure occurs or provide historical failed run IDs.
 - **No STAR/alignment task data yet:** Both runs are still in early stages (QC/trim). Resource pressure and potential OOM failures during STAR genome generation and alignment are not yet observable.
 - **No cost data:** Neither run has completed, so total run cost is unavailable. Individual task costs are in the $0.001–$0.007 range for early QC tasks.
-
diff --git a/.seqera/context/HISTORY.md b/.seqera/context/HISTORY.md
@@ -48,7 +48,6 @@
 
 Both runs are concurrent nf-core/rnaseq executions on the same workspace with identical test data (GM12878_REP1, GM12878_REP2). Key differences:
 
-
 | Metric                  | 1cF65l2PDvxNd5                       | 5VGC0gjEmghOaz             |
 | ----------------------- | ------------------------------------ | -------------------------- |
 | Submit time             | 17:51:26Z                            | 17:50:14Z                  |
@@ -58,7 +57,6 @@ Both runs are concurrent nf-core/rnaseq executions on the same workspace with id
 | FQ_LINT avg realtime    | ~605s                                | ~613s                      |
 | Cost pattern            | Slightly higher per-task (m5d.large) | Lower per-task (c5d.large) |
 
-
 The timing variance in short tasks (SAMTOOLS_FAIDX: 28s vs 62s) likely reflects spot instance variability and S3 staging latency rather than algorithmic differences. Both runs are still in progress — STAR genome generation and alignment phases are pending.
 
 ## Local Development History (git log)
@@ -69,4 +67,3 @@ Recent development has focused on the **benchmark report rendering pipeline**:
 2. **Combined runtime charts** (18a64f4 → a49a9a4): Added combined task runtime visualisation with scheduling overhead, per-pipeline breakdowns, and ECharts integration
 3. **CUR cost streaming** (b96ecfd): Optimised AWS CUR parquet processing with batch streaming
 4. **Test colocation** (96b8b81): Moved benchmark tests to live alongside their modules
-
diff --git a/.seqera/context/PATTERNS.md b/.seqera/context/PATTERNS.md
@@ -93,7 +93,6 @@ Early QC tasks cost $0.001–$0.007 each. The dominant cost will come from STAR
 
 ## File Naming Conventions
 
-
 | Pattern                | Convention                                  |
 | ---------------------- | ------------------------------------------- |
 | Modules                | `modules/local/<name>/main.nf`              |
@@ -104,11 +103,9 @@ Early QC tasks cost $0.001–$0.007 each. The dominant cost will come from STAR
 | Bin scripts            | `bin/benchmark_report_<stage>.py`           |
 | Agent docs             | `AGENTS.md` at each directory level         |
 
-
 ## Git Workflow
 
 - Feature branches named `<user>/<description>`
 - Conventional commits: `feat()`, `fix()`, `test()`, `refactor()`, `docs()`, `perf()`
 - Commit signing required (GPG via SSH/1Password)
 - Pre-commit hooks for linting
-
diff --git a/.seqera/context/PIPELINE.md b/.seqera/context/PIPELINE.md
@@ -39,29 +39,24 @@ Input CSV (id, workspace, group, logs, platform, token_env)
 
 ## Entry Points
 
-
 | File                             | Role                                                                             |
 | -------------------------------- | -------------------------------------------------------------------------------- |
 | `main.nf`                        | Pipeline entry — validates params, parses samplesheet, delegates to NF_AGGREGATE |
 | `workflows/nf_aggregate/main.nf` | Core workflow — branching, API fetch, process chaining                           |
 | `lib/SeqeraApi.groovy`           | Groovy API client — paginated task fetch, workspace resolution                   |
 | `bin/benchmark_report.py`        | Typer CLI — normalize-jsonl, aggregate-report-data, render-html, fetch           |
 
-
 ## Processes (4 local modules)
 
-
 | Process                           | Container                       | Input                                       | Output                      |
 | --------------------------------- | ------------------------------- | ------------------------------------------- | --------------------------- |
 | `EXTRACT_TARBALL`                 | ubuntu:22.04                    | `(meta, tarball)`                           | `(meta, dir)` of JSON files |
 | `NORMALIZE_BENCHMARK_JSONL`       | wave python/duckdb/jinja2/typer | `data_dir`, `cur_parquet`                   | `jsonl_bundle/`             |
 | `AGGREGATE_BENCHMARK_REPORT_DATA` | wave python/duckdb/jinja2/typer | `jsonl_bundle/`                             | `report_data.json`          |
 | `RENDER_BENCHMARK_REPORT`         | wave python/duckdb/jinja2/typer | `report_data.json`, `brand.yml`, `logo.svg` | `benchmark_report.html`     |
 
-
 ## Key Parameters
 
-
 | Parameter                   | Default                       | Purpose                                     |
 | --------------------------- | ----------------------------- | ------------------------------------------- |
 | `input`                     | required                      | CSV samplesheet of run IDs / external paths |
@@ -72,7 +67,6 @@ Input CSV (id, workspace, group, logs, platform, token_env)
 | `java_truststore_path`      | `null`                        | Custom Java truststore for private certs    |
 | `java_truststore_password`  | `null`                        | Truststore password                         |
 
-
 ## Input Schema
 
 CSV with columns: `id` (required), `workspace` (required, `org/name` or `external`), `group` (optional), `logs` (path to tarball/dir for external), `platform` (per-row API URL override), `token_env` (per-row env var name for bearer token).
@@ -99,4 +93,3 @@ results/
 3. **All JSON files** are collected into a single temp directory and passed to the 3-stage Python pipeline: normalize → aggregate → render.
 4. The Python stages are separate Nextflow processes sharing one Wave container image (`python_duckdb_jinja2_typer_pruned`).
 5. JSONL is the handoff format — streaming-friendly for large run datasets and Fusion FS compatible.
-
diff --git a/.seqera/skills/fetch-and-compare-platform-runs/SKILL.md b/.seqera/skills/fetch-and-compare-platform-runs/SKILL.md
@@ -6,6 +6,7 @@ description: >
   benchmark candidates, refreshing `.seqera/context`, or validating run-level
   differences before building a report.
 ---
+
 # Fetch and compare Platform runs
 
 Use this skill when the user wants to inspect one or more Seqera Platform runs
@@ -78,4 +79,3 @@ Build a full benchmark report when:
 - the user wants charts or HTML output
 - cost and aggregated process summaries matter more than raw run inspection
 - you need JSONL handoff artifacts for downstream debugging
-
diff --git a/AGENTS.md b/AGENTS.md
@@ -66,10 +66,10 @@ uv run --with typer --with pyyaml \
 
 ### Services overview
 
-| Service | Purpose | Run command |
-|---------|---------|-------------|
-| Nextflow pipeline | Core product — aggregates metrics from Seqera Platform runs | `nextflow run . --input <csv> --outdir results -profile docker` |
-| Python benchmark_report.py | Normalizes JSON -> JSONL, aggregates report data, then renders HTML | See "Rebuild Command" section above |
+| Service                    | Purpose                                                             | Run command                                                     |
+| -------------------------- | ------------------------------------------------------------------- | --------------------------------------------------------------- |
+| Nextflow pipeline          | Core product — aggregates metrics from Seqera Platform runs         | `nextflow run . --input <csv> --outdir results -profile docker` |
+| Python benchmark_report.py | Normalizes JSON -> JSONL, aggregates report data, then renders HTML | See "Rebuild Command" section above                             |
 
 ### Running tests
 
diff --git a/docs/DESIGN.md b/docs/DESIGN.md
@@ -36,6 +36,7 @@ python bin/benchmark_report.py normalize-jsonl --data-dir <run_json_dir> --outpu
 ```
 
 Responsibilities:
+
 - read run JSON payloads
 - normalize runs/tasks/metrics rows
 - optionally normalize CUR parquet into `costs.jsonl`
@@ -54,6 +55,7 @@ python bin/benchmark_report.py aggregate-report-data --jsonl-dir <jsonl_bundle>
 ```
 
 Responsibilities:
+
 - stream JSONL rows
 - compute report sections:
   - `benchmark_overview`
@@ -75,13 +77,15 @@ python bin/benchmark_report.py render-html --data <report_data.json> --output <b
 ```
 
 Responsibilities:
+
 - load report JSON
 - apply brand/logo overrides when provided
 - render self-contained HTML from the Jinja template
 
 ## Benchmark CLI surface
 
 `bin/benchmark_report.py` provides:
+
 - `normalize-jsonl`
 - `aggregate-report-data`
 - `render-html`
diff --git a/modules/local/AGENTS.md b/modules/local/AGENTS.md
@@ -2,13 +2,14 @@
 
 Each module should keep one clear responsibility and its own terse `AGENTS.md`.
 
-| Module                                  | Status     | Purpose                                        |
-| --------------------------------------- | ---------- | ---------------------------------------------- |
-| `normalize_benchmark_jsonl/`            | **active** | Raw run JSON (+ optional CUR parquet) → JSONL |
-| `aggregate_benchmark_report_data/`      | **active** | JSONL bundle → `report_data.json`              |
-| `render_benchmark_report/`              | **active** | `report_data.json` + branding → HTML           |
-| `extract_tarball/`                      | active     | Extract run-data tarballs for external runs    |
+| Module                             | Status     | Purpose                                       |
+| ---------------------------------- | ---------- | --------------------------------------------- |
+| `normalize_benchmark_jsonl/`       | **active** | Raw run JSON (+ optional CUR parquet) → JSONL |
+| `aggregate_benchmark_report_data/` | **active** | JSONL bundle → `report_data.json`             |
+| `render_benchmark_report/`         | **active** | `report_data.json` + branding → HTML          |
+| `extract_tarball/`                 | active     | Extract run-data tarballs for external runs   |
 
 Testing
+
 - Keep stage-specific pytest tests beside the module under `tests/`.
 - Keep pipeline routing/integration scenarios under top-level `tests/`.
diff --git a/modules/local/aggregate_benchmark_report_data/AGENTS.md b/modules/local/aggregate_benchmark_report_data/AGENTS.md
@@ -1,26 +1,32 @@
 # aggregate_benchmark_report_data
 
 Purpose
+
 - Convert the JSONL bundle into a single `report_data.json` document for rendering.
 
 Owns
+
 - `AGGREGATE_BENCHMARK_REPORT_DATA` in `main.nf`
 - Module-local CLI entrypoint in `bin/benchmark_report.py`
 - Shared aggregation logic in repo-root `bin/benchmark_report_aggregate.py`
 - Stage-scoped tests under `tests/`
 
 Run directly
+
 - `nextflow run modules/local/aggregate_benchmark_report_data/main.nf -profile docker,arm --jsonl_bundle <jsonl_bundle_dir>`
 - The direct `nextflow run modules/local/...` path depends on the module-local `bin/benchmark_report.py` shim/CLI; keep that invocation shape working if you refactor the stage.
 
 Inputs
+
 - `jsonl_bundle/` from `normalize_benchmark_jsonl`
 
 Outputs
+
 - `report_data.json`
 - `versions.yml`
 
 Invariants
+
 - This is the boundary between streaming records and presentation data.
 - Prefer streaming iteration over JSONL inputs; avoid full-file eager loads unless clearly bounded.
 - Cost joins must key by `(run_id, process, hash)` to avoid cross-process collisions.
@@ -36,8 +42,10 @@ Invariants
   - `cost_overview`
 
 Edit guidance
+
 - Keep rendering/template logic out of this stage.
 - If output schema changes, update render tests and any HTML assertions.
 
 Tests
+
 - `pytest modules/local/aggregate_benchmark_report_data/tests/test_aggregate.py -q`
diff --git a/modules/local/extract_tarball/AGENTS.md b/modules/local/extract_tarball/AGENTS.md
@@ -1,21 +1,27 @@
 # extract_tarball
 
 Purpose
+
 - Extract external run-data tarballs into directories of JSON artifacts.
 
 Owns
+
 - `EXTRACT_TARBALL` in `main.nf`
 
 Inputs
+
 - external tarball paths from the workflow routing layer
 
 Outputs
+
 - extracted directory per tarball
 - `versions.yml`
 
 Invariants
+
 - Extraction only. Do not mix benchmark parsing or aggregation into this module.
 - Downstream workflow code is responsible for collecting JSON files from extracted directories.
 
 Edit guidance
+
 - If tarball layout assumptions change, update the pipeline tarball scenario tests.
diff --git a/modules/local/normalize_benchmark_jsonl/AGENTS.md b/modules/local/normalize_benchmark_jsonl/AGENTS.md
@@ -1,41 +1,49 @@
 # normalize_benchmark_jsonl
 
 Purpose
+
 - Normalize collected run JSON into a stream-friendly `jsonl_bundle/`.
 
 Owns
+
 - `NORMALIZE_BENCHMARK_JSONL` in `main.nf`
 - Module-local CLI entrypoint in `bin/benchmark_report.py`
 - Shared normalization logic in repo-root `bin/benchmark_report_normalize.py`
 - Stage-scoped tests under `tests/`
 
 Run directly
+
 - `nextflow run modules/local/normalize_benchmark_jsonl/main.nf -profile docker,arm --data_dir <dir> --benchmark_aws_cur_report <parquet-or-NO_FILE>`
 - The direct `nextflow run modules/local/...` path depends on the module-local `bin/benchmark_report.py` shim/CLI; keep that invocation shape working if you refactor the stage.
 
 Inputs
+
 - `data_dir/` of per-run JSON payloads
 - optional CUR parquet
 
 Outputs
+
 - `jsonl_bundle/runs.jsonl`
 - `jsonl_bundle/tasks.jsonl`
 - `jsonl_bundle/metrics.jsonl`
 - optional `jsonl_bundle/costs.jsonl`
 - `versions.yml`
 
 Invariants
+
 - JSONL is the handoff format for Fusion-friendly streaming.
 - One JSON object per line.
 - Task rows should already include derived fields needed downstream (`process_short`, `wait_ms`, `staging_ms`).
 - Failed tasks are filtered here so downstream stages stay simple.
 
 Edit guidance
+
 - Keep this stage about normalization only; no report aggregation or HTML concerns.
 - If you change row shape, update:
   - `bin/benchmark_report_normalize.py`
   - `modules/local/aggregate_benchmark_report_data/tests/test_aggregate.py`
   - any CLI compatibility tests affected
 
 Tests
+
 - `pytest modules/local/normalize_benchmark_jsonl/tests/test_normalize.py -q`
diff --git a/modules/local/render_benchmark_report/AGENTS.md b/modules/local/render_benchmark_report/AGENTS.md
@@ -1,35 +1,43 @@
 # render_benchmark_report
 
 Purpose
+
 - Render self-contained HTML from `report_data.json` plus branding assets.
 
 Owns
+
 - `RENDER_BENCHMARK_REPORT` in `main.nf`
 - Module-local CLI entrypoint in `bin/benchmark_report.py`
 - Shared render logic in repo-root `bin/benchmark_report_render.py`
 - Stage-scoped tests under `tests/`
 
 Run directly
+
 - `nextflow run modules/local/render_benchmark_report/main.nf -profile docker,arm --report_data_json <report_data.json> --brand_yml <brand.yml-or-NO_FILE> --logo_svg <logo.svg-or-NO_FILE>`
 - The direct `nextflow run modules/local/...` path depends on the module-local `bin/benchmark_report.py` shim/CLI; keep that invocation shape working if you refactor the stage.
 
 Inputs
+
 - `report_data.json`
 - optional `brand.yml`
 - optional logo SVG
 
 Outputs
+
 - `benchmark_report.html`
 - `versions.yml`
 
 Invariants
+
 - Rendering consumes precomputed report data only.
 - No raw JSON normalization or report aggregation should happen here.
 - Keep template input contract stable unless you also update the renderer tests and report template.
 
 Edit guidance
+
 - Prefer changing `report_data.json` upstream over adding data-massaging logic in the template.
 - Branding/theme lookup should stay tolerant of missing optional assets.
 
 Tests
+
 - `pytest modules/local/render_benchmark_report/tests/test_render.py -q`
diff --git a/renovate.json b/renovate.json
@@ -1,4 +1,4 @@
 {
-  "$schema": "https://docs.renovatebot.com/renovate-schema.json",
-  "baseBranches": ["dev"]
+    "$schema": "https://docs.renovatebot.com/renovate-schema.json",
+    "baseBranches": ["dev"]
 }
diff --git a/tests/AGENTS.md b/tests/AGENTS.md
@@ -1,6 +1,7 @@
 # tests/
 
 ## Layout
+
 Each pipeline-level scenario lives in its own directory:
 
 - `pipeline_api_only/`
@@ -9,18 +10,21 @@ Each pipeline-level scenario lives in its own directory:
 - `pipeline_benchmark_directory/`
 
 Each scenario directory contains:
+
 - `main.nf.test` — the nf-test scenario
 - `main.nf.test.snap` — the snapshot for that scenario
 - `AGENTS.md` — scenario-specific guidance for future edits
 
 ## Conventions
+
 - One scenario per directory.
 - Keep assertions local and explicit rather than heavily abstracted.
 - Prefer stable fixture files under `workflows/nf_aggregate/assets/`.
 - If routing behavior changes, update the scenario-specific `AGENTS.md` along with the test.
 - This directory is for pipeline routing/integration scenarios only; stage-specific pytest tests now live beside the relevant module under `modules/local/*/tests/`.
 
 ## Running tests
+
 Run all pipeline-level scenario tests with:
 
 ```bash
diff --git a/tests/pipeline_api_only/AGENTS.md b/tests/pipeline_api_only/AGENTS.md
@@ -1,16 +1,20 @@
 # pipeline_api_only
 
 ## Purpose
+
 Covers the API-only input path when `generate_benchmark_report` is disabled.
 
 ## Fixtures
+
 - `workflows/nf_aggregate/assets/test_run_ids.csv`
 
 ## Expected behavior
+
 - No Nextflow processes should run.
 - A warning should explain that API runs produce no output without benchmark generation.
 - Only `pipeline_info/collated_software_versions.yml` should be emitted.
 - No `benchmark_report/` directory should exist.
 
 ## Edit guidance
+
 If you change API-only routing, benchmark gating, or warning text, update this test first.
diff --git a/tests/pipeline_benchmark_directory/AGENTS.md b/tests/pipeline_benchmark_directory/AGENTS.md
diff --git a/tests/pipeline_benchmark_tarball/AGENTS.md b/tests/pipeline_benchmark_tarball/AGENTS.md
diff --git a/tests/pipeline_mixed_no_benchmark/AGENTS.md b/tests/pipeline_mixed_no_benchmark/AGENTS.md
diff --git a/workflows/nf_aggregate/assets/log_dirs/15dvxY1LnZYrYe/15dvxY1LnZYrYe.json b/workflows/nf_aggregate/assets/log_dirs/15dvxY1LnZYrYe/15dvxY1LnZYrYe.json
diff --git a/workflows/nf_aggregate/main.nf b/workflows/nf_aggregate/main.nf
