merge(07-02): bring in workflow wrapper, test JSON, and Dockstore entry

Author: carze

.dockstore.yml

@@ -333,4 +333,7 @@ workflows:
     primaryDescriptorPath: /pipes/WDL/workflows/classify_virnucpro_multi.wdl
   - name: align_and_generate_reads_report
     subclass: WDL
-    primaryDescriptorPath: /pipes/WDL/workflows/align_and_generate_PAF.wdl
+    primaryDescriptorPath: /pipes/WDL/workflows/align_and_generate_PAF.wdl
+  - name: join_read_classifications
+    subclass: WDL
+    primaryDescriptorPath: /pipes/WDL/workflows/join_read_classifications.wdl

.planning/REQUIREMENTS.md

@@ -72,18 +72,18 @@
 
 ### Standalone Workflow
 
-- [ ] **JRC-02**: Standalone workflow `pipes/WDL/workflows/join_read_classifications.wdl`
+- [x] **JRC-02**: Standalone workflow `pipes/WDL/workflows/join_read_classifications.wdl`
   - Imports `tasks_metagenomics.wdl`, calls task with alias `as join_reads`
   - `meta { allowNestedInputs: true }` for Terra-compatible test JSON
   - Passes `miniwdl check` validation
 
 ### Infrastructure
 
-- [ ] **JRC-03**: Test input JSON `test/input/WDL/miniwdl-local/test_inputs-join_read_classifications-local.json`
+- [x] **JRC-03**: Test input JSON `test/input/WDL/miniwdl-local/test_inputs-join_read_classifications-local.json`
   - Placeholder paths for all 4 optional File inputs plus sample_id
   - Workflow-level input keys; follows existing test file conventions
 
-- [ ] **JRC-04**: Dockstore registration entry in `.dockstore.yml` for `join_read_classifications.wdl`
+- [x] **JRC-04**: Dockstore registration entry in `.dockstore.yml` for `join_read_classifications.wdl`
   - Subclass: WDL
   - No `testParameterFiles` (placeholder paths not CI-runnable)
 

.planning/ROADMAP.md

@@ -115,7 +115,7 @@ Plans:
 | 4. Core centrifuger Task | v3.0 | 1/1 | Complete   | 2026-04-02 |
 | 5. centrifuger_single and centrifuger_multi Workflow Wrappers | v3.0 | 1/1 | Complete   | 2026-04-02 |
 | 6. Test Input JSONs and Dockstore Registration | v3.0 | 1/1 | Complete   | 2026-04-02 |
-| 7. join_read_classifications Task, Workflow, and Registration | v3.1 | 0/2 | Planning | - |
+| 7. join_read_classifications Task, Workflow, and Registration | v3.1 | 1/2 | In Progress|  |
 
 ---
 *Last updated: 2026-04-02 — Phase 7 planned*

.planning/STATE.md

@@ -3,15 +3,15 @@ gsd_state_version: 1.0
 milestone: v1.0
 milestone_name: milestone
 current_phase: 07
-status: executing
-stopped_at: Completed 07-01-PLAN.md
-last_updated: "2026-04-02T21:32:52.208Z"
+status: verifying
+stopped_at: Completed 07-02-PLAN.md
+last_updated: "2026-04-02T21:39:26.485Z"
 last_activity: 2026-04-02
 progress:
   total_phases: 4
-  completed_phases: 3
-  total_plans: 5
-  completed_plans: 4
+  completed_phases: 2
+  total_plans: 4
+  completed_plans: 3
   percent: 0
 ---
 
@@ -30,7 +30,7 @@ Phase: 07 (turn-join-read-classifications-py-script-into-a-wdl-pipeline-task-in-
 Plan: 2 of 2
 Milestone: v3.0 Centrifuger Taxonomic Classification WDL
 Current phase: 07
-Status: Ready to execute
+Status: Phase complete — ready for verification
 Last activity: 2026-04-02
 
 Progress: [░░░░░░░░░░] 0% (0/3 phases complete)
@@ -65,6 +65,8 @@ Recent decisions affecting current work:
 - [Phase 05]: Sample names derived from basename(bam, .bam) inside bash loop — String sample_name input removed
 - [Phase 06]: No testParameterFiles on centrifuger Dockstore entries — placeholder paths not CI-runnable
 - [Phase 07]: join_read_classifications task in tasks_metagenomics.wdl — File? optional inputs with __NONE__ sentinel, 16 GB/1 CPU runtime, DuckDB 4-way FULL OUTER JOIN logic embedded verbatim
+- [Phase 07]: Call alias as join_reads — WDL disallows call name = containing workflow name (per D-10)
+- [Phase 07]: No testParameterFiles in Dockstore entry for join_read_classifications — placeholder paths not CI-runnable
 
 ### Pending Todos
 
@@ -83,7 +85,7 @@ None.
 
 ## Session Continuity
 
-Last session: 2026-04-02T21:32:52.205Z
-Stopped at: Completed 07-01-PLAN.md
+Last session: 2026-04-02T21:39:22.390Z
+Stopped at: Completed 07-02-PLAN.md
 Resume file: None
 Next action: `/gsd:plan-phase 4`

.planning/phases/07-turn-join-read-classifications-py-script-into-a-wdl-pipeline-task-in-task-utils/07-02-SUMMARY.md

@@ -0,0 +1,117 @@
+---
+phase: 07-turn-join-read-classifications-py-script-into-a-wdl-pipeline-task-in-task-utils
+plan: 02
+subsystem: metagenomics
+tags: [wdl, dockstore, workflow-wrapper, parquet, kallisto, kraken2, virnucpro, genomad]
+
+# Dependency graph
+requires:
+  - phase: 07-01
+    provides: join_read_classifications WDL task in tasks_metagenomics.wdl
+provides:
+  - join_read_classifications standalone workflow wrapper
+  - Placeholder test input JSON for join_read_classifications
+  - Dockstore registration entry for join_read_classifications
+affects:
+  - Dockstore discoverability of join_read_classifications on Terra/DNAnexus
+
+# Tech tracking
+tech-stack:
+  added: []
+  patterns:
+    - Standalone workflow wrapper importing tasks_metagenomics.wdl with task alias (as join_reads)
+    - allowNestedInputs: true for Terra-compatible placeholder test JSON
+
+key-files:
+  created:
+    - pipes/WDL/workflows/join_read_classifications.wdl
+    - test/input/WDL/miniwdl-local/test_inputs-join_read_classifications-local.json
+  modified:
+    - .dockstore.yml
+
+key-decisions:
+  - "Call alias as join_reads — WDL disallows call name = containing workflow name (D-10)"
+  - "No testParameterFiles in Dockstore entry — placeholder paths not CI-runnable (D-09)"
+  - "allowNestedInputs: true — required for Terra-compatible test JSON with workflow-level input keys"
+
+patterns-established:
+  - "Workflow wrapper with task alias avoids call-name = workflow-name collision"
+
+requirements-completed:
+  - JRC-02
+  - JRC-03
+  - JRC-04
+
+# Metrics
+duration: 2min
+completed: 2026-04-02
+---
+
+# Phase 7 Plan 02: join_read_classifications Workflow Wrapper Summary
+
+**Standalone workflow wrapper + placeholder test JSON + Dockstore entry for join_read_classifications — completing full task+workflow+test+registration treatment consistent with all prior phases**
+
+## Performance
+
+- **Duration:** 2 min
+- **Started:** 2026-04-02T21:37:02Z
+- **Completed:** 2026-04-02T21:38:35Z
+- **Tasks:** 2
+- **Files modified:** 3
+
+## Accomplishments
+
+- Created `join_read_classifications.wdl` workflow wrapper importing `tasks_metagenomics.wdl` and calling the task with alias `join_reads` (per D-10)
+- Added `allowNestedInputs: true` in meta block for Terra-compatible test JSON
+- All 4 optional `File?` inputs and required `String sample_id` passed through to task; `classifications_parquet` exposed as workflow output
+- `miniwdl check` exits 0 with no errors
+- Created placeholder test input JSON with workflow-level keys for all 5 inputs
+- Appended `join_read_classifications` entry to `.dockstore.yml` with `subclass: WDL`, no `testParameterFiles`
+
+## Task Commits
+
+Each task was committed atomically:
+
+1. **Task 1: Create standalone workflow wrapper** - `d05801d0` (feat)
+2. **Task 2: Create test input JSON and Dockstore entry** - `a812d49b` (feat)
+
+## Files Created/Modified
+
+- `pipes/WDL/workflows/join_read_classifications.wdl` - Standalone workflow wrapper (33 lines)
+- `test/input/WDL/miniwdl-local/test_inputs-join_read_classifications-local.json` - Placeholder test JSON (7 lines)
+- `.dockstore.yml` - Appended join_read_classifications entry (3 lines added)
+
+## Decisions Made
+
+- Used call alias `as join_reads` — WDL disallows a call with the same name as the enclosing workflow. This follows the established pattern (`parse_reads`, `classify_contigs`, `classify_reads`).
+- No `testParameterFiles` in Dockstore entry — placeholder paths are not CI-runnable (consistent with all prior phase entries per STATE.md decision log).
+- `allowNestedInputs: true` added to meta — required for Terra to accept the `workflow.input` key format in test JSON.
+
+## Deviations from Plan
+
+None - plan executed exactly as written.
+
+## Issues Encountered
+
+None.
+
+## User Setup Required
+
+None - no external service configuration required.
+
+## Next Phase Readiness
+
+- Phase 07 is complete — `join_read_classifications` task + workflow + test + registration fully implemented
+- The workflow is discoverable on Dockstore and callable as a standalone workflow on Terra/DNAnexus
+
+## Self-Check: PASSED
+
+- FOUND: pipes/WDL/workflows/join_read_classifications.wdl
+- FOUND: test/input/WDL/miniwdl-local/test_inputs-join_read_classifications-local.json
+- FOUND: join_read_classifications entry in .dockstore.yml
+- FOUND: commit d05801d0
+- FOUND: commit a812d49b
+
+---
+*Phase: 07-turn-join-read-classifications-py-script-into-a-wdl-pipeline-task-in-task-utils*
+*Completed: 2026-04-02*

pipes/WDL/workflows/join_read_classifications.wdl

@@ -0,0 +1,33 @@
+version 1.0
+
+import "../tasks/tasks_metagenomics.wdl" as metagenomics
+
+workflow join_read_classifications {
+    meta {
+        description: "Join read-level classifications from Kallisto, Kraken2, VirNucPro, and geNomad into a single ZSTD-compressed Parquet file keyed on SAMPLE_ID + READ_ID."
+        author: "Broad Viral Genomics"
+        email:  "viral-ngs@broadinstitute.org"
+        allowNestedInputs: true
+    }
+
+    input {
+        File?   kallisto_summary
+        File?   kraken2_reads
+        File?   vnp_reads
+        File?   genomad_virus_summary
+        String  sample_id
+    }
+
+    call metagenomics.join_read_classifications as join_reads {
+        input:
+            kallisto_summary      = kallisto_summary,
+            kraken2_reads         = kraken2_reads,
+            vnp_reads             = vnp_reads,
+            genomad_virus_summary = genomad_virus_summary,
+            sample_id             = sample_id
+    }
+
+    output {
+        File classifications_parquet = join_reads.classifications_parquet
+    }
+}

test/input/WDL/miniwdl-local/test_inputs-join_read_classifications-local.json

@@ -0,0 +1,7 @@
+{
+  "join_read_classifications.kallisto_summary": "test/input/placeholder_kallisto_summary.parquet",
+  "join_read_classifications.kraken2_reads": "test/input/placeholder_kraken2_reads.parquet",
+  "join_read_classifications.vnp_reads": "test/input/placeholder_vnp_reads.parquet",
+  "join_read_classifications.genomad_virus_summary": "test/input/placeholder_genomad_virus_summary.tsv",
+  "join_read_classifications.sample_id": "placeholder_sample"
+}