fix: Issue cleanup

Makefile

@@ -1,28 +1,18 @@
 PYTHON ?= python3
 ZENSICAL ?= zensical
 
-.PHONY: update-branches
-update-branches:
-	@echo "Updating GitHub branch links in docs..."
-	@$(PYTHON) scripts/update_doc_links.py
-
-.PHONY: prepare
-prepare:
-	@$(PYTHON) scripts/prepare_docs.py
-
 .PHONY: build
-build: prepare
+build:
 	@$(ZENSICAL) build --clean
 
 .PHONY: serve
-serve: prepare
+serve:
 	@$(ZENSICAL) serve
 
 .PHONY: help
 help:
 	@echo "Makefile targets:"
-	@echo "  prepare           - Stage local docs plus imported upstream tool docs into .generated/docs"
 	@echo "  build             - Build the Zensical site with the active Python environment"
 	@echo "  serve             - Serve the Zensical site with the active Python environment"
-	@echo "  update-branches   - Update docs to point to configured development branches for repos"
 	@echo "  help              - Show this message"
+

docs/calypr/project-management/calypr-admin/approve-requests.md

@@ -64,7 +64,7 @@ We use Gen3's role based access control (RBAC) to manage access to data.
   * /programs/ucl
   * /programs/manchester
 
-Designated users within each institution have privileges to update requests. "Update" in this context means setting the status of a user's request to [SIGNED].
+Designated users within each institution have privileges to update requests. "Update" in this context means setting the status of a user's request to `SIGNED`.
 
 Since this approach relies on Gen3's [Requestor](https://github.com/uc-cdis/requestor/blob/master/docs/functionality_and_flow.md#example-backend-flow) for all assignments of policies to users we get  the following benefits:
 

docs/tools/funnel/docs/compute/gcp-batch.md

@@ -6,23 +6,37 @@ menu:
     weight: 20
 ---
 
-!!! warning "Current Limitations ⚠️"
-    - Latest Funnel release ([v0.11.11](https://github.com/ohsu-comp-bio/funnel/releases/tag/v0.11.11)) requires specific bucket prefixing in the inputs and outputs
-      - e.g. `/mnt/disks/<BUCKET>/<FILE>` instead of `/<FILE>`
-    - Nextflow workflows are currently not supported (as Nextflow expects root-level working directories → `/work`)
-
 # Overview
 
-The following steps illustrate how to run a TES tasks via GCP Batch utilizing Google Storage Buckets.
+The following steps illustrate how to run TES tasks via GCP Batch utilizing Google Storage Buckets.
+
+GCS buckets are automatically mounted inside task containers. Input and output paths use standard filesystem paths (e.g. `/input/file.txt`) — no `/mnt/disks/` prefixing required. Nextflow workflows are supported via the TES executor `workdir` field.
 
 # Quick Start
 
+## 1. Download Funnel
+
 ```sh
-curl -fsSL https://calypr.github.io/funnel/install.sh | bash
+curl -fsSL https://calypr.org/funnel/install.sh | bash
+```
+
+## 2. Start Server
+
+<details>
+  <summary><code>Config Example</code></summary>
 
-funnel server run --Compute "gcp-batch"                \
-                  --GCPBatch.Project "example-project" \
-                  --GCPBatch.Location "us-central1"
+```yaml
+Compute: gcp-batch
+
+GCPBatch:
+  Project: example-project
+  Location: us-central1
+```
+
+</details>
+
+```sh
+funnel server run --Compute "gcp-batch" --GCPBatch.Project "example-project" --GCPBatch.Location "us-central1"
 ```
 
 ## 3. Submit Task
@@ -35,22 +49,23 @@ funnel server run --Compute "gcp-batch"                \
   "name": "Input/Output Test",
   "inputs": [
     {
-      "url": "gs://tes-batch-integration/README.md",
-      "path": "/mnt/disks/tes-batch-integration/README.md"
+      "url": "gs://my-bucket/input/README.md",
+      "path": "/input/README.md"
     }
   ],
   "outputs": [
     {
-      "url": "gs://tes-batch-integration/README.md.sha256",
-      "path": "/mnt/disks/tes-batch-integration/README.md.sha256"
+      "url": "gs://my-bucket/output/README.md.sha256",
+      "path": "/output/README.md.sha256"
     }
   ],
   "executors": [
     {
       "image": "alpine",
       "command": [
-        "sha256sum",
-        "/mnt/disks/tes-batch-integration/README.md | tee /mnt/disks/tes-batch-integration/README.md.sha256"
+        "sh",
+        "-c",
+        "sha256sum /input/README.md | tee /output/README.md.sha256"
       ]
     }
   ]
@@ -75,24 +90,25 @@ funnel task get <TASK ID>
   "executors": [
     {
       "command": [
-        "sha256sum",
-        "/mnt/disks/tes-batch-integration/README.md | tee /mnt/disks/tes-batch-integration/README.md.sha256"
+        "sh",
+        "-c",
+        "sha256sum /input/README.md | tee /output/README.md.sha256"
       ],
       "image": "alpine"
     }
   ],
   "id": "d6f0tgpurbu7o23pgj20",
   "inputs": [
     {
-      "path": "/mnt/disks/tes-batch-integration/README.md",
-      "url": "gs://tes-batch-integration/README.md"
+      "path": "/input/README.md",
+      "url": "gs://my-bucket/input/README.md"
     }
   ],
-  "name": "GCP Batch Task Example",
+  "name": "Input/Output Test",
   "outputs": [
     {
-      "path": "/mnt/disks/tes-batch-integration/README.md.sha256",
-      "url": "gs://tes-batch-integration/README.md.sha256"
+      "path": "/output/README.md.sha256",
+      "url": "gs://my-bucket/output/README.md.sha256"
     }
   ],
   "state": "COMPLETE"
@@ -102,8 +118,24 @@ funnel task get <TASK ID>
 ## 5. Verify Outputs
 
 ```sh
-gsutil cat gs://tes-batch-integration/README.md.sha256
-9b9916cea5348edd6ad78893231edb81fc96772d1dd99fae9c2a64f84646cb1c  /mnt/disks/tes-batch-integration/README.md
+gsutil cat gs://my-bucket/output/README.md.sha256
+9b9916cea5348edd6ad78893231edb81fc96772d1dd99fae9c2a64f84646cb1c  /input/README.md
+```
+
+# Nextflow
+
+Nextflow tasks can specify a working directory via the TES executor `workdir` field, which maps to Docker's `--workdir` flag inside the GCP Batch container:
+
+```json
+{
+  "executors": [
+    {
+      "image": "nextflow/nextflow:latest",
+      "command": ["nextflow", "run", "main.nf"],
+      "workdir": "/work"
+    }
+  ]
+}
 ```
 
 # Additional Resources

docs/tools/funnel/docs/compute/grid-engine.md

@@ -54,4 +54,3 @@ The following variables are available for use in the template:
 
 See https://golang.org/pkg/text/template for information on creating templates.
 
-[ge]: http://gridscheduler.sourceforge.net/documentation.html

docs/tools/funnel/docs/development/developers.md

@@ -36,7 +36,7 @@ A Funnel development environment includes:
 - [gRPC Gateway][gateway] for HTTP communication.
 - [Angular][angular] and [SASS][sass] for the web dashboard.
 - [GNU Make][make] for development tasks.
-- [Docker][docker] for executing task containers (tested with v1.12, v1.13).
+- [Docker](https://docker.io) for executing task containers (tested with v1.12, v1.13).
 - [dep][dep] for Go dependency vendoring.
 - [Make][make] for development/build commands.
 - [NodeJS][node] and [NPM][npm] for web dashboard development.
@@ -64,8 +64,6 @@ mock interfaces in test code, for example, to mock the Google Cloud APIs.
 [grpc]: http://www.grpc.io/
 [sass]: http://sass-lang.com/
 [make]: https://www.gnu.org/software/make/
-[docker]: https://docker.io
-[python]: https://www.python.org/
 [dep]: https://golang.github.io/dep/
 [node]: https://nodejs.org
 [npm]: https://www.npmjs.com/

docs/tools/funnel/docs/download.md

@@ -32,4 +32,3 @@ Funnel requires Go 1.21+. Check out the [development docs][dev] for more detail.
 
 
 [dev]: ./development/developers.md
-[docker]: https://docker.io

docs/tools/funnel/docs/metrics/prometheus.md

@@ -32,5 +32,4 @@ Funnel exports these metrics:
   of bytes of disk space available by all nodes.
 
 [prom]: https://prometheus.io/
-[gauge]: https://prometheus.io/docs/concepts/metric_types/#gauge
 [graf]: https://grafana.com/

docs/tools/grip/docs/clients.md

@@ -89,13 +89,13 @@ This represents the vertex we queried for above. All vertexes in the system will
 * _\_id_: This represents the global identifier for this vertex. In order to draw edges between different vertexes from different data sets we need an identifier that can be constructed from available data. Often, the `_id` will be the field that you query on as a starting point for a traversal.
 * _\_label_: The label represents the type of the vertex. All vertexes with a given label will share many property keys and edge labels, and form a logical group within the system.
 
-The data on a query result can be accessed as properties on the result object; for example `result[0].data.symbol` would return:
+The data on a query result can be accessed as properties on the result object; for example `result[0].data.symbol` would return:
 
 ```python
 u'TP53'
 ```
 
-You can also do a `has` query with a list of items using `gripql.within([...])` (other conditions exist, see the `Conditions` section below):
+You can also do a `has` query with a list of items using `gripql.within([...])` (other conditions exist, see the `Conditions` section below):
 
 ```python
 result = G.V().hasLabel("Gene").has(gripql.within("symbol", ["TP53", "BRCA1"])).render({"_id": "_id", "symbol":"symbol"}).execute()

docs/tools/grip/docs/databases.md

@@ -104,7 +104,7 @@ Drivers:
 
 # SQLite
 
-GRIP supports storing vertices and edges in [SQLite]
+GRIP supports storing vertices and edges in [SQLite](https://sqlite.org/)
 
 Config:
 
@@ -116,5 +116,3 @@ Drivers:
     Sqlite:
       DBName: tester/sqliteDB
 ```
-
-[psql]: https://sqlite.org/

docs/tools/grip/docs/queries/jsonpath.md

@@ -60,11 +60,11 @@ Below is a table of field and the values they would reference in subsequent trav
 | _id                       | "NM_007294.3:c.4963_4981delTGGCCTGACCCCAGAAG" |
 | _label                     | "variant"            |
 | type                       | "deletion"           |
-| publications[0].pmid       | 29480828             |
-| publications[:].pmid       | [29480828, 23666017] |
-| publications.pmid          | [29480828, 23666017] |
-| $gene.symbol.hugo          | "BRCA1"              |
-| $gene.transcripts[0]       | "ENST00000471181.7"  |
+| `publications[0].pmid`     | 29480828             |
+| `publications[:].pmid`     | `[29480828, 23666017]` |
+| `publications.pmid`        | `[29480828, 23666017]` |
+| `$gene.symbol.hugo`        | "BRCA1"              |
+| `$gene.transcripts[0]`     | "ENST00000471181.7"  |
 
 
 ## Usage Example:

docs/tools/sifter/docs/inputs/sqldump.md

@@ -11,7 +11,7 @@ Scan file produced produced from sqldump.
 | Name | Type | Description |
 |-------|---|--------|
 | path | string | Path to the SQL dump file | 
-| tables | []string | Names of tables to read out |
+| tables | `[]string` | Names of tables to read out |
 
 ## Example
 

docs/tools/sifter/docs/inputs/table.md

@@ -13,7 +13,7 @@ Extract data from tabular file, includiong TSV and CSV files.
 |-------|---|--------|
 | path     |   string   | File to be transformed |
 |	rowSkip   |   int       | Number of header rows to skip | 
-|	columns   |   []string  | Manually set names of columns |
+|	columns   |   `[]string`  | Manually set names of columns |
 |	extraColumns | string   |  Columns beyond originally declared columns will be placed in this array |
 |	sep       |   string   | Separator \\t for TSVs or , for CSVs |
 

docs/tools/sifter/docs/transforms/clean.md

@@ -14,7 +14,7 @@ Remove fields that don't appear in the desingated list.
 
 | name | Type | Description |
 | --- | --- | --- |
-| fields | [] string | Fields to keep | 
+| fields | `[]string` | Fields to keep | 
 | removeEmpty | bool | Fields with empty values will also be removed |
 | storeExtra | string | Field name to store removed fields |
 

docs/tools/sifter/docs/transforms/fieldProcess.md

@@ -14,7 +14,7 @@ each of the items in the array will become an independent row.
 | name | Type | Description |
 | --- | --- | --- |
 | field | string | Name of field to be processed |
-| mapping | map[string]string | Project templated values into child element |
+| mapping | `map[string]string` | Project templated values into child element |
 | itemField | string | If processing an array of non-dict elements, create a dict as `{itemField:element}` |
 
 

docs/tools/sifter/docs/transforms/lookup.md

@@ -12,7 +12,7 @@ Using key from current row, get values from a reference source
 | --- | --- | --- |
 | replace | string (field path) | Field to replace | 
 | lookup | string (template string) | Key to use for looking up data |
-| copy | map[string]string | Copy values from record that was found by lookup. The Key/Value record uses the Key as the destination field and copies the field from the retrieved records using the field named in Value |  
+| copy | `map[string]string` | Copy values from record that was found by lookup. The Key/Value record uses the Key as the destination field and copies the field from the retrieved records using the field named in Value |  
 | tsv | TSVTable  | TSV translation table file | 
 | json | JSONTable | JSON data file | 
 | table | LookupTable | Inline lookup table | 

docs/tools/sifter/docs/transforms/project.md

@@ -12,8 +12,8 @@ Populate row with templated values
 
 | name | Type | Description |
 | --- | --- | --- |
-| mapping | map[string]any | New fields to be generated from template |
-| rename | map[string]string | Rename field (no template engine) |
+| mapping | `map[string]any` | New fields to be generated from template |
+| rename | `map[string]string` | Rename field (no template engine) |
 
 
 # Example

docs/tools/sifter/docs/transforms/reduce.md

@@ -18,7 +18,7 @@ Using key from rows, reduce matched records into a single entry
 | method | string | Method name |
 | python | string | Python code string |
 | gpython | string | Python code string run using (https://github.com/go-python/gpython) |
-| init | map[string]any | Data to use for first reduce | 
+| init | `map[string]any` | Data to use for first reduce | 
 
 ## Example
 

netlify.toml

@@ -1,3 +1,3 @@
 [build]
-  command = "python scripts/prepare_docs.py && zensical build --clean"
+  command = "zensical build --clean"
   publish = "site"

requirements.txt

@@ -1,2 +1,3 @@
 zensical
 termynal
+mkdocs-multirepo-plugin