fix: redirect links to individual wf pages, minor update usage instructions (#40)

* fix: dynamic re-routing of old to new workflow pages

* fix: updated deployment options: apptainer in favor of singularity

* fix: change space to slash in workflow links and pages

Author: m-jahn

README.md

@@ -40,19 +40,19 @@ In order to additionally appear in the "standardized usage" area, repositories a
 
 Typical content of the `.snakemake-workflow-catalog.yml` file:
 
-```bash
+```yaml
 usage:
-  mandatory-flags: # optional definition of additional flags
-    desc: # describe your flags here in a few sentences (they will be inserted below the example commands)
+  mandatory-flags:
+    desc: # describe your flags here in a few sentences
     flags: # put your flags here
-  software-stack-deployment: # definition of software deployment method (at least one of conda, singularity, or singularity+conda)
-    conda: true # whether pipeline works with --use-conda
-    singularity: true # whether pipeline works with --use-singularity
-    singularity+conda: true # whether pipeline works with --use-singularity --use-conda
-    report: true # add this to confirm that the workflow allows to use 'snakemake --report report.zip' to generate a report containing all results and explanations
+  software-stack-deployment:
+    conda: true # whether pipeline works with '--sdm conda'
+    apptainer: true # whether pipeline works with '--sdm apptainer/singularity'
+    apptainer+conda: true # whether pipeline works with '--sdm conda apptainer/singularity'
+    report: true # whether creation of reports using 'snakemake --report report.zip' is supported
 ```
 
-Once included in the standardized usage area you can link directly to the usage instructions for your repository via the URL `https://snakemake.github.io/snakemake-workflow-catalog?usage=<owner>/<repo>`.
+Once included in the standardized usage area you can link directly to the workflow page using the URL `https://snakemake.github.io/snakemake-workflow-catalog/docs/workflows/<owner>/<repo>`. Do not forget to replace the `<owner>` and `<repo>` tags at the end of the URL.
 
 ### Release handling
 

source/_static/redirect.js

@@ -0,0 +1,14 @@
+document.addEventListener("DOMContentLoaded", function () {
+  const params = new URLSearchParams(window.location.search);
+  const usage = params.get("usage");
+
+  if (usage) {
+    // Dynamically construct the target URL
+    const targetUrl = `docs/workflows/${usage}.html`;
+
+    // Redirect to the dynamically constructed URL
+    window.location.href = targetUrl;
+  } else {
+    console.error("No usage parameter found in the URL.");
+  }
+});

source/_templates/all_standardized_workflows.md

@@ -9,7 +9,7 @@
 :widths: auto
 
 {% for repo in input -%}
-    [{{ repo["full_name"] }}](<workflows/{{ repo["md"] }}>){% raw %},{% endraw %}
+    [{{ repo["full_name"] }}](<workflows/{{ repo["full_name"] }}>){% raw %},{% endraw %}
     "{{ repo["description"] }}"{% raw %},{% endraw %}
     {%- for t in repo["topics"] -%}{bdg-secondary}`{{ t }}` {% endfor %}{% raw %},{% endraw %}
     {bdg-muted}`last update {{ repo["last_update"] }}`

source/_templates/workflows_by.md

@@ -4,7 +4,7 @@
 
 {% for repo in input -%}
 
-:::{grid-item-card} [{{ repo["name"] }}](<workflows/{{ repo["md"] }}>)
+:::{grid-item-card} [{{ repo["name"] }}](<workflows/{{ repo["full_name"] }}>)
 
 {{ repo["user"] }}
 
@@ -40,6 +40,6 @@
 :hidden:
 
 {% for repo in input -%}
-workflows/{{ repo["user"] }} {{ repo["name"] }}
+workflows/{{ repo["full_name"] }}
 {% endfor %}
 ```

source/build_wf_pages.py

@@ -60,7 +60,6 @@ def build_wf_pages():
         repo = repos[current_repo]
         wf_data = {}
         wf_data["full_name"] = current_repo
-        md_filename = f"{current_repo.replace('/', ' ')}.md"
         # prepare title, description, reporting, qc stats, etc.
         wf_data["description"] = repo["description"]
         wf_data["topics"] = repo["topics"]
@@ -75,8 +74,10 @@ def build_wf_pages():
         wf_data["config_from_readme"] = check_readme(repo["config_readme"])
         # render and export
         md_rendered = template.render(wf=wf_data)
-        output_dir = Path("docs/workflows")
-        output_path = output_dir / md_filename
+        output_dir = Path(f"docs/workflows/{current_repo.split('/')[0]}")
+        if not output_dir.exists():
+            output_dir.mkdir(parents=True, exist_ok=True)
+        output_path = output_dir / f"{current_repo.split('/')[1]}.md"
         with open(output_path, "w", encoding="utf-8") as f:
             f.write(md_rendered)
 

source/build_wf_tables.py

@@ -77,7 +77,6 @@ def build_wf_tables():
         repos = {}
         for repo in json.loads(f.read()):
             repo = {k: repo[k] for k in selected_items if k in repo}
-            repo["md"] = repo["full_name"].replace("/", " ")
             repo["user"] = repo["full_name"].split("/")[0]
             repo["name"] = repo["full_name"].split("/")[1]
             last_update = datetime.fromtimestamp(repo["updated_at"])

source/conf.py

@@ -71,13 +71,6 @@
 }
 
 # -- Manage redirection of old to new wf pages -------------------------------
-# these are simply static redirects without wildcards
-rendered_wfs = os.listdir("docs/workflows")
-redirects = {}
-for wf in rendered_wfs:
-    if not wf.endswith(".md"):
-        continue
-    wf_items = wf.replace(".md", "").split(" ")
-    redirects[f"?usage={wf_items[0]}%2F{wf_items[1]}"] = (
-        f"docs/workflows/{wf_items[0]} {wf_items[1]}"
-    )
+html_js_files = [
+    "redirect.js",
+]

source/docs/about/adding_workflows.md

@@ -29,8 +29,8 @@ usage:
     flags: # put your flags here
   software-stack-deployment:
     conda: true # whether pipeline works with '--sdm conda'
-    singularity: true # whether pipeline works with '--sdm singularity/apptainer'
-    singularity+conda: true # whether pipeline works with '--sdm conda singularity/apptainer'
+    apptainer: true # whether pipeline works with '--sdm apptainer/singularity'
+    apptainer+conda: true # whether pipeline works with '--sdm conda apptainer/singularity'
     report: true # whether creation of reports using 'snakemake --report report.zip' is supported
 ```
 
@@ -42,7 +42,7 @@ Definition of mandatory flags can happen through a list of strings (`['--a', '--
 The content of the `.snakemake-workflow-catalog.yml` file is subject to change. Flags might change in the near future, but current versions will always stay compatible with the catalog. 
 :::
 
-Once included in the standardized usage area you can link directly to the usage instructions for your repository via the URL `https://snakemake.github.io/snakemake-workflow-catalog?usage=<owner>/<repo>`. Do not forget to replace the `<owner>` and `<repo>` tags at the end of the URL.
+Once included in the standardized usage area you can link directly to the workflow page using the URL `https://snakemake.github.io/snakemake-workflow-catalog/docs/workflows/<owner>/<repo>`. Do not forget to replace the `<owner>` and `<repo>` tags at the end of the URL.
 
 ### Release handling
 

source/index.md

@@ -66,7 +66,7 @@ Explore workflows 🔭
 
 ## Contributing
 
-- Improving PRs or issues with the workflow catalog (only the catalog, not the workflows themselves) can be made [here](http://github.com/snakemake/snakemake-plugin-catalog)
+- Improving PRs or issues with the workflow catalog (only the catalog, not the workflows themselves) can be made [here](http://github.com/snakemake/snakemake-workflow-catalog)
 - Improving PRs or issues with the listed workflows can be made at the respective workflow repository (see indivuidual [workflow pages](<docs/all_standardized_workflows>)).
 - Resources for creating new workflows can be found [here](<docs/snakemake>) or in more detail on the [Snakemake documnentation](https://snakemake.readthedocs.io/en/stable/index.html)
 - New workflows will be [automatically added](<docs/catalog>) to the workflow catalog if they are contained in eligible Github repositories