forgot to add new script (#45)

patch fix for #44

workflow/scripts/generate_aggregate_qc.py

@@ -0,0 +1,27 @@
+from jinja2 import Environment, FileSystemLoader
+from pathlib import Path
+
+datasets = snakemake.params.datasets
+total_html = snakemake.output.total_html
+subj_htmls = snakemake.input.subj_htmls
+
+# load jinja template
+file_loader = FileSystemLoader(".")
+env = Environment(loader=file_loader)
+template = env.get_template(snakemake.input.report_html)
+
+output = template.render()
+
+for i,subj_html in enumerate(subj_htmls):
+    subject=datasets.loc[i,'subject']
+    sample=datasets.loc[i,'sample']
+    acq=datasets.loc[i,'acq']
+
+    relative_path = Path(subj_html).relative_to(Path(total_html).parent)
+    # Create line to add link to subject into final qc report combining all subjects
+    subj_link = f'\n\t\t<a href="{relative_path}">sub-{subject}_sample-{sample}_acq-{acq}</a><br>\n'
+
+    output+=subj_link
+
+with open(total_html, 'w') as f:
+    f.write(output)