broadinstitute
diff --git a/‎.dockstore.yml‎
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diff --git a/‎AGENTS.md‎
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diff --git a/‎CLAUDE.md‎
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diff --git a/‎README.md‎
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diff --git a/‎docs/WDL_STYLE_RULES.md‎
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@@ -0,0 +1,23 @@
+version: 1.2
+
+# Dockstore registration for HVP-LR workflows.
+# Reference: https://docs.dockstore.org/en/stable/getting-started/dockstore-yml.html
+
+workflows:
+  - name: HifiReadQCPipeline
+    subclass: WDL
+    primaryDescriptorPath: /wdl/pipelines/PacBio/QC/HifiReadQCPipeline.wdl
+    readMePath: /README.md
+    authors:
+      - name: Jonn Smith
+        orcid: 0000-0002-4279-8220
+        affiliation: Broad Institute
+      - name: Terrance Shea
+        orcid: 0000-0002-6586-9298
+        affiliation: Broad Institute
+    filters:
+      branches:
+        - main
+        - /jts_.*/
+      tags:
+        - /.*/
@@ -180,7 +180,9 @@ Trivy runs twice per image: once as a build gate (table format, `exit-code: 1`),
 
 Override the threshold per repo via the `TRIVY_LARGE_IMAGE_BYTES` GitHub Actions repository variable.
 
-## WDL validation
+## WDL style + validation
+
+Style rules (file layout, boilerplate, task skeleton, naming, output ordering, `t_NN_` call aliasing, etc.) live in [docs/WDL_STYLE_RULES.md](docs/WDL_STYLE_RULES.md). Read it before writing or reformatting any `.wdl` file.
 
 The `miniwdl check --strict` pre-commit hook is the **only** WDL gate. There is no CI safety net. If a contributor commits without running pre-commit (`git commit -n`), broken WDLs land on `main`.
 
@@ -233,6 +235,7 @@ Concurrency: `release-main` group, no cancel-in-progress.
 
 ## Adding a new WDL — checklist
 
+0. Read [docs/WDL_STYLE_RULES.md](docs/WDL_STYLE_RULES.md) — file layout, task skeleton, naming, call aliasing.
 1. Write under `wdl/<workflow>.wdl`.
 2. (Optional) Inputs JSON alongside as `wdl/<workflow>.inputs.json`.
 3. Run `miniwdl check --strict wdl/<workflow>.wdl` locally. The pre-commit hook runs the same.
 
@@ -1,6 +1,6 @@
 # CLAUDE.md
 
-**Before doing any work in this repo, read [AGENTS.md](AGENTS.md) in its entirety.** Then read [CONTRIBUTING.md](CONTRIBUTING.md).
+**Before doing any work in this repo, read [AGENTS.md](AGENTS.md) in its entirety.** Then read [CONTRIBUTING.md](CONTRIBUTING.md). **Before touching any `.wdl` file, also read [docs/WDL_STYLE_RULES.md](docs/WDL_STYLE_RULES.md).**
 
 This is not optional and not skippable for "small" or "obvious" changes. Many file edits in this repo look trivial but have non-obvious CI consequences:
 
 
@@ -10,9 +10,14 @@ HVP-LR/
 │   └── <image>/                  #   (Dockerfile, Makefile, env.yaml, .dockerignore,
 │                                 #    .trivyignore, .trivy-ignore-policy.rego)
 ├── wdl/                          # WDL workflow definitions
+│   ├── structs/Structs.wdl       #   Shared RuntimeAttr struct
+│   ├── tasks/<Category>/         #   Task modules (Preprocessing, QC, Utility, ...)
+│   └── pipelines/<Tech>/<Cat>/   #   End-to-end workflows (<Tech> = PacBio | ONT | ILMN | TechAgnostic)
+├── docs/                         # Project docs (WDL style rules, etc.)
 ├── scripts/                      # CI helper scripts
 ├── .github/workflows/            # docker.yml (build/push/scan), cd.yml (release)
 ├── .pre-commit-config.yaml       # WDL validation hook
+├── .dockstore.yml                # Dockstore workflow registration manifest
 ├── dev-requirements.txt          # Local dev tooling
 ├── VERSION                       # Repo-level version
 ├── LICENSE                       # MIT License
@@ -27,14 +32,16 @@ HVP-LR/
 | What | Where |
 |------|-------|
 | A new Docker image | `docker/<image-name>/` |
-| A new WDL workflow or task | `wdl/<workflow>.wdl` |
-| A workflow's inputs JSON | `wdl/<workflow>.inputs.json` (alongside the WDL) |
+| A new task module | `wdl/tasks/<Category>/<Name>.wdl` |
+| A new pipeline / workflow | `wdl/pipelines/<Tech>/<Category>/<Name>.wdl` |
+| A workflow's inputs JSON | Alongside the WDL as `<Name>.inputs.json` |
 | Helper / one-off scripts | `scripts/` (avoid if not CI-related; otherwise put inside the relevant `docker/<image>/`) |
 
 ## Where to read next
 
 - **Setting up locally / opening a PR** → [CONTRIBUTING.md](CONTRIBUTING.md)
 - **CI mechanics, Docker conventions, releases, Trivy filtering, hard rules** → [AGENTS.md](AGENTS.md)
+- **WDL style rules** (file layout, task skeleton, naming, call aliasing) → [docs/WDL_STYLE_RULES.md](docs/WDL_STYLE_RULES.md)
 - **License terms** → [LICENSE](LICENSE)
 
 If you're an AI agent (Claude or otherwise), start with [CLAUDE.md](CLAUDE.md) / [AGENTS.md](AGENTS.md).
@@ -47,6 +54,14 @@ If you're an AI agent (Claude or otherwise), start with [CLAUDE.md](CLAUDE.md) /
 
 Images are published to `ghcr.io/broadinstitute/hvp-lr/<image>:<version>` and (when GCR is configured) `us.gcr.io/broadinstitute/<image>:<version>`. GHCR packages are private by default.
 
+## Current workflows
+
+| Workflow | Path | Purpose |
+|----------|------|---------|
+| `HifiReadQCPipeline` | `wdl/pipelines/PacBio/QC/HifiReadQCPipeline.wdl` | Single-sample PacBio HiFi read QC: taxonomy lookup, BAM→FASTQ, seqkit + kraken2 stats, per-sample human-readable report |
+
+Workflows are registered with Dockstore via [.dockstore.yml](.dockstore.yml).
+
 ## License
 
 MIT — see [LICENSE](LICENSE). The LICENSE file is bundled into every built container at `/opt/hvp-lr/LICENSE`. If you redistribute the source or an image, MIT requires the copyright notice and license text to travel with it.
@@ -81,7 +81,7 @@ task ExampleTask {
         set -euxo pipefail
 
         # ---- Resource detection (required preamble) ----
-        NUM_CPUS=$(cat /proc/cpuinfo | grep '^processor' | tail -n1 | awk '{print $NF+1}')
+        NUM_CPUS=$(grep '^processor' /proc/cpuinfo | tail -n1 | awk '{print $NF+1}')
         RAM_IN_GB=$(free -g | grep "^Mem" | awk '{print $2}')
 
         # Reserve 1 GB for OS + container overhead.
@@ -386,7 +386,7 @@ Insert immediately after `set -euxo pipefail`:
 set -euxo pipefail
 
 # ---- Resource detection (required preamble) ----
-NUM_CPUS=$(cat /proc/cpuinfo | grep '^processor' | tail -n1 | awk '{print $NF+1}')
+NUM_CPUS=$(grep '^processor' /proc/cpuinfo | tail -n1 | awk '{print $NF+1}')
 RAM_IN_GB=$(free -g | grep "^Mem" | awk '{print $2}')
 
 # Reserve 1 GB for OS + container overhead.