WIP: fixing qc so flatfieldqc isn't enabled with prestitched

- while I am at it, will change jinja rules to maybe use snakemake built-in jinja
khanlab · Sep 8, 2024 · d7a3543 · d7a3543
1 parent ce66e0e
commit d7a3543
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Showing 2 changed files with 11 additions and 12 deletions.
diff --git a/resources/qc/subject_html_temp.html b/resources/qc/subject_html_temp.html
@@ -4,10 +4,9 @@
         <title>{{ subject }} - {{ sample }} - {{ acq }}</title>
     </head>
     <body>
+        {% for link_path, link_description in zip(link_paths, link_descriptions) %}
+        <a href="{{ link_path }}">{{ link_description }}</a><br>
+        {% endfor %}
         <a href="{{ back_link }}">Back</a><br>
-        <a href="{{ ffhtml }}">Flatfield Correction QC</a><br>
-        <a href="{{ wshtml }}">Whole Slice QC</a>
-        <br>
-        <a href="{{ volhtml }}">Volume Rendered Image</a>
     </body>
-</html>
+</html>
diff --git a/workflow/scripts/generate_subject_qc.py b/workflow/scripts/generate_subject_qc.py
@@ -8,9 +8,10 @@
 template = env.get_template(snakemake.input.subject_html)
 
 # input html files
-ws_html = snakemake.input.ws_html
-ff_html = snakemake.input.ff_html
-vol_html = snakemake.input.vol_html
+in_htmls = snakemake.input.in_htmls
+#ws_html = snakemake.input.ws_html
+#ff_html = snakemake.input.ff_html
+#vol_html = snakemake.input.vol_html
 
 # output html files
 sub_html = snakemake.output.sub_html
@@ -22,13 +23,12 @@
 
 # Get relative path to the subjects QC htmls
 
-ws_rel_path = Path(ws_html).relative_to(Path(sub_html).parent)
-ff_rel_path = Path(ff_html).relative_to(Path(sub_html).parent)
-vol_rel_path = Path(vol_html).relative_to(Path(sub_html).parent)
+link_rel_paths = [ Path(link_path).relative_to(Path(sub_html).parent) for link_path in snakemake.input.link_paths]
+link_descriptions = snakemake.params.link_descriptions
 
 # Fill in jinja template for subject html and write it out
 output = template.render(back_link="../qc_report.html",subject=subject,sample=sample,acq=acq,
-                         ffhtml=ff_rel_path,wshtml=ws_rel_path, volhtml=vol_rel_path)
+                         link_rel_paths, link_descriptions)
 with open(sub_html, 'w') as f:
     f.write(output)