Add nf-core/eager fixture + compare-and-contrast scenario against iwc#1234

content/pipelines/nextflow-to-galaxy/scenarios.md

@@ -25,6 +25,115 @@ fixtures with `make fixtures-nextflow`.
   per step (discover or author); the partial scope is stated explicitly rather
   than silently dropping the remaining pipeline.
 
+## Case: nf-core/eager vs. a human-authored aDNA workflow (compare and contrast)
+
+A **reference case**, not a matching test. galaxyproject/iwc#1234 ("Add
+nf-core/eager style ancient DNA (aDNA) analysis workflow", human-authored by Mert
+Aydın) targets the same source pipeline this journey converts, so it gives us a
+hand-built answer to hold the machine's answer against. The journey will never
+reproduce it, and shouldn't try — the value is in *where* and *why* the two
+diverge. Nothing here is a pass/fail gate; the pipeline oracle in `eval.md` still
+supplies the actual gates.
+
+Three caveats to keep the comparison honest:
+
+- **Version boundary.** The PR's README cites `nf-co.re/eager/2.5.3/` — eager
+  2.x, which is DSL1 and therefore out of scope for [[summarize-nextflow]]. The
+  fixture pins the DSL2 rewrite on `dev` (3.x). The aDNA tool vocabulary is
+  substantially the same across the two, so the contrast is meaningful, but this
+  is not a controlled A/B and per-step differences may be version artifacts
+  rather than authoring differences.
+- **Not in the corpus.** The PR is unmerged, so `paleogenomics/adna-analysis`
+  does not exist at the pinned IWC SHA. [[compare-against-iwc-exemplar]] cannot
+  reach it and will settle on some other exemplar; that phase's output is not the
+  comparison. Supply the PR out-of-band by URL when doing the write-up, per the
+  URL-not-mirror principle — do not mirror the `.ga` into the repo.
+- **Human ≠ correct.** The PR is open and unreviewed. Where the journey diverges,
+  either side may be the better answer.
+
+- fixture: `workflow-fixtures/pipelines/nf-core__eager` (DSL2 `dev` pin; large —
+  ~110 `.nf` files, ~45 nf-core modules, ~23 local subworkflows).
+- reference: <https://github.com/galaxyproject/iwc/pull/1234>, workflow
+  `paleogenomics/adna-analysis`.
+- expect (gated by `eval.md`): eager is a toolkit, not a linear pipeline — its
+  schema exposes ~15 independent `run_*`/`skip_*` branch groups (preprocessing,
+  mapping, bam_filtering, deduplication, damage_manipulation,
+  adna_damage_analysis, genotyping, metagenomics, contamination_estimation,
+  human_sex_determination, consensus_sequence, host_removal, …). The journey must
+  reach a **stated scope decision** about which branches it carries, and say so
+  explicitly rather than silently flattening the toolkit into whichever path the
+  template happened to take.
+
+  A scope decision that freezes *every* branch into one hardcoded path satisfies
+  the letter of that and misses the point: eager's optionality is much of what
+  eager is, and a conversion that discards all of it has answered an easier
+  question than the one asked. So the bar is that some meaningful part of the
+  source's branch surface reaches the user as **run-time choice** — a workflow an
+  analyst can steer without editing it. Which choices, how many, and by what
+  mechanism are the journey's call, and a defensible small set beats a large one.
+  The point is that the collapse to a single frozen path should have to be argued
+  for, not fallen into.
+
+  Deliberately not prescribed: the reference keeps four user-facing controls and
+  spends 12 `when` steps doing it, but that is **calibration, not a quota** —
+  evidence that this much optionality is reachable in gxformat2 at all. A journey
+  that keeps three different controls, or reaches the same coverage through
+  optional inputs rather than `when` gating, passes. A journey that pads its count
+  with toggles eager's schema doesn't motivate fails on intent-fidelity — the
+  optionality has to be earned by the source, not manufactured to hit a number.
+- contrast (advisory; record, don't gate):
+  - **Which branches survive as branches.** The PR is conditional-rich by IWC
+    standards: 52 steps, of which 12 carry a `when`. It keeps four user-facing
+    branch controls — `Choose Read Type` (SE/PE), `Choose Mapper` (BWA/Bowtie2),
+    and two optional-input conditionals (HapMap present → ANGSD X-contamination;
+    BED present → Sex.DetERRmine variant) — while hardcoding one pick for
+    preprocessing (AdapterRemoval), dedup (Picard MarkDuplicates), genotyping
+    (FreeBayes), profiling (Kraken2), and damage (mapDamage). Note the line drawn
+    is *not* "data-flow shape stays, tool-swap goes": the mapper switch is a tool
+    swap and survives. The kept set reads closer to "choices an aDNA analyst
+    actually makes at runtime". Does the journey's scope decision land on a
+    comparable set, and on what principle?
+  - **The conditional plumbing tax.** Galaxy has no native if/else, so eager's
+    toggles are paid for structurally: 7 `map_param_value` steps turn selections
+    and optional-input presence into `when` booleans, and 6 `pick_value` steps
+    rejoin the branches — 13 of 41 tool steps (~⅓) are param plumbing, not
+    science. The pattern is duplicate-per-branch + gate + merge (`AdapterRemoval
+    (Single-End)`/`(Paired-End)`, `Map with BWA`/`Bowtie2`). Record what the
+    journey does here rather than scoring it against this idiom — duplicate-gate-
+    merge is one known-workable answer, not the sanctioned one, and a cheaper
+    route to the same run-time coverage would be a finding worth having. The tax
+    is also the honest argument *for* a narrower scope: ~⅓ of the step budget
+    going to plumbing is a real cost, and a journey that cites it while keeping
+    fewer controls has reasoned, not given up. A worked human example of that
+    trade priced out in full is the main reason this case earns its keep.
+  - **Where the human answer looks arguable.** Steps 39/40 (Sex.DetERRmine
+    with/without BED) are *both* registered workflow outputs, as are both ANGSD
+    paths — so any given run yields outputs that are necessarily empty. If the
+    journey avoids that, it is not automatically wrong for differing from the
+    reference.
+  - **Which branches were dropped entirely.** No circularmapper, malt/megan,
+    metaphlan, krakenuniq, pmdtools, multivcfanalyzer/consensus, pileupcaller, or
+    mapad in the PR. Does the journey's scope decision land on a comparable
+    subset, and does it justify the cut?
+  - **Tool resolution.** Per `eval.md`, every tool is discovered or authored. The
+    human found Shed wrappers for the whole aDNA set (EndorSpy, Sex.DetERRmine,
+    MtNucRatioCalculator, mapDamage included). Where the journey chose to *author*
+    a wrapper for something that already exists in the Shed, that's a
+    discover-shed-tool recall gap worth filing.
+  - **Interface shape.** The human surfaced ~10 named inputs with prose-legible
+    labels and pushed eager's flag sprawl into defaults. Compare against what the
+    interface brief produced — count, naming, and how much of the ~200-param
+    surface leaked through.
+  - **Test strategy.** The PR ships a Planemo suite on sub-sampled `JK2067` /
+    `hs37d5` / HapMap data. Compare against what
+    [[nextflow-test-to-galaxy-test-plan]] → [[implement-galaxy-workflow-test]]
+    produce — did the journey reach real aDNA fixtures, or synthesize? This is
+    the case most likely to expose the pipeline's known test-data gap: the spine
+    has no [[find-test-data]] phase, so `implement-galaxy-workflow-test` takes
+    `test-data-refs` with nothing upstream producing it (the validator warns on
+    exactly this). aDNA reference data is heavy and non-obvious; if the gap bites
+    anywhere, it bites here.
+
 ## Case: branch-control fidelity
 
 - fixture: a Nextflow summary with a skip-style branch control (e.g.

workflow-fixtures/fixtures.yaml

@@ -91,6 +91,22 @@ pipelines:
       branching, different domain from rnaseq/sarek — stresses the
       incompatibility report on parallel-tool patterns.
 
+  - name: nf-core/eager
+    flavor: nf-core
+    tier: large
+    repo: https://github.com/nf-core/eager.git
+    sha: f77d2464a7c6fe06b67ce1832f2fe72ba21c8fde
+    notes: >
+      Ancient DNA (aDNA) analysis. Pinned to the DSL2 rewrite on `dev`
+      (eager 3.x), NOT to a release: the latest tag (2.5.3) is DSL1
+      (`nextflow.enable.dsl=1`, monolithic main.nf), which
+      summarize-nextflow short-circuits by design. Bump the SHA rather
+      than adding a `tag` until 3.0 ships. Large: ~110 .nf files, ~45
+      nf-core modules, ~23 local subworkflows; damage-profiling and
+      metagenomics branches on top of a preprocess/map/dedup spine.
+      Backs the compare-and-contrast case in the NEXTFLOW → GALAXY
+      pipeline scenarios against galaxyproject/iwc#1234.
+
   # ----- ref-data complexity bridge (nf-core) -----
   # Small/medium pipelines staged on rungs of a reference-data
   # complexity ladder. Used to scope which ref-data patterns the