Output HTML for review pipeline

Edinburgh-Genome-Foundry · Oct 16, 2024 · da51f6d · da51f6d
1 parent b5f9faf
commit da51f6d
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Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/ediacara/reports.py b/ediacara/reports.py
@@ -45,7 +45,7 @@ def end_pug_to_html(template, **context):
     return pug_to_html(template, **context)
 
 
-def write_assembly_analysis_report(target, assemblybatch):
+def write_assembly_analysis_report(pdf_file, html_file, assemblybatch):
     """Write a sequencing run report with a PDF summary.
 
 
@@ -69,7 +69,9 @@ def write_assembly_analysis_report(target, assemblybatch):
     html = end_pug_to_html(
         ASSEMBLY_ANALYSIS_REPORT_TEMPLATE, assemblybatch=assemblybatch
     )
-    write_report(html, target, extra_stylesheets=(STYLESHEET,))
+    with open(html_file, "w") as html_output:
+        html_output.write(html)
+    write_report(html, pdf_file, extra_stylesheets=(STYLESHEET,))
 
 
 def write_sequencinggroup_report(pdf_file, html_file, sequencinggroup):

diff --git a/tests/test_reports.py b/tests/test_reports.py
@@ -89,6 +89,7 @@ def test_write_assembly_analysis_report(tmpdir):
     assembly_plan_path = os.path.join(data_dir, "review", "assembly_plan.csv")
     params_projectname = "Test review"
     pdf_file = os.path.join(str(tmpdir), "review_report.pdf")
+    html_file = os.path.join(str(tmpdir), "review_report.html")
 
     entries = pd.read_csv(samplesheet_csv, header=None)
     entries.columns = [
@@ -120,4 +121,4 @@ def test_write_assembly_analysis_report(tmpdir):
     )
     assemblybatch.perform_all_interpretations_in_group()
 
-    edi.write_assembly_analysis_report(pdf_file, assemblybatch)
+    edi.write_assembly_analysis_report(pdf_file, html_file, assemblybatch)