Fix a bug with caching of report assets

CHANGELOG.rst

@@ -13,6 +13,7 @@ v2.3.1-dev
 * **Breaking change**: Update the json output format
 * **Breaking change**: Update Snakemake to version 8
 * Fix a bug with the Java runtime environment for Picard
+* Fix a bug with caching of report assets introduced in snakemake 8
 * Run VarDict job with 8 threads
 
 **********

Snakefile

@@ -183,9 +183,6 @@ rule generate_report:
         scr=workflow.source_path("scripts/generate_report.py"),
         # Ensure all report files are localised to the stupid Snakemake cache
         report_files=report_files,
-    params:
-        templates="report/templates",
-        imgs="report/assets/img",
     output:
         "{sample}/hamlet_report.{sample}.pdf",
     log:
@@ -194,9 +191,15 @@ rule generate_report:
         containers["hamlet-scripts"]
     shell:
         """
+        # Find the cached location of the report folder
+        css={input.css}
+        report=${{css%assets/style.css}}
+        templates="${{report}}templates"
+        imgs="${{report}}imgs"
+
         python3 {input.scr} \
-            --templates-dir {params.templates} \
-            --imgs-dir {params.imgs} \
+            --templates-dir ${{templates}} \
+            --imgs-dir ${{imgs}} \
             --css-path {input.css} \
             --toc-path {input.toc} \
             {input.summary} \
@@ -211,9 +214,8 @@ rule generate_html_report:
         css=workflow.source_path("report/assets/style.css"),
         toc=workflow.source_path("report/assets/toc.xsl"),
         scr=workflow.source_path("scripts/generate_report.py"),
-    params:
-        templates="report/templates",
-        imgs="report/assets/img",
+        # Ensure all report files are localised to the stupid Snakemake cache
+        report_files=report_files,
     output:
         "{sample}/hamlet_report.{sample}.html",
     log:
@@ -222,9 +224,15 @@ rule generate_html_report:
         containers["hamlet-scripts"]
     shell:
         """
+        # Find the cached location of the report folder
+        css={input.css}
+        report=${{css%assets/style.css}}
+        templates="${{report}}templates"
+        imgs="${{report}}imgs"
+
         python3 {input.scr} \
-            --templates-dir {params.templates} \
-            --imgs-dir {params.imgs} \
+            --templates-dir ${{templates}} \
+            --imgs-dir ${{imgs}} \
             --css-path {input.css} \
             --toc-path {input.toc} \
             {input.summary} \

common.smk

@@ -17,24 +17,26 @@ containers = {
 }
 
 
-def list_files(folder) -> list[str]:
-    """Recursively list all files in folder"""
-    files = list()
-
-    for item in os.listdir(folder):
-        path = os.path.join(folder, item)
-        if os.path.isfile(path):
-            files.append(path)
-        elif os.path.isdir(path):
-            files += list_files(path)
-        else:
-            msg = f"Unknown path: {path=}"
-            raise RuntimeError(msg)
-    return files
-
-
 def report_files(wildcards):
-    return list_files("report")
+    files = [
+        "report/templates/contents_about.html.j2",
+        "report/templates/contents_aln.html.j2",
+        "report/templates/contents_basic.html.j2",
+        "report/templates/contents_fusion.html.j2",
+        "report/templates/contents_var.html.j2",
+        "report/templates/cover.html.j2",
+        "report/templates/contents.html.j2",
+        "report/templates/contents_itd.html.j2",
+        "report/templates/contents_rna.html.j2",
+        "report/templates/contents_overview.html.j2",
+        "report/assets/style.css",
+        "report/assets/toc.xsl",
+        "report/assets/img/hamlet-logo.jpg",
+        "report/assets/img/lumc-logo.jpg",
+        "report/assets/img/Myeloblast_logo.png",
+    ]
+
+    return [workflow.source_path(fname) for fname in files]
 
 
 # The version of HAMLET