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public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/pdf_report.py

@@ -403,6 +403,7 @@ class GentrapLib(object):
         self._raw = summary
         # flexiprep settings
         self.flexiprep = summary.get("flexiprep", {})
+        self.flexiprep_files = summary.get("flexiprep", {}).get("files", {}).get("pipeline", {})
         self.clipping = not self.flexiprep["settings"]["skip_clip"]
         self.trimming = not self.flexiprep["settings"]["skip_trim"]
         self.is_paired_end = self.flexiprep["settings"]["paired"]

public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/lib.tex

 \section{Library "((( lib.name )))" Results}
 \label{lib:(((lib.name)))}
 
+\subsection{Input information}
+\label{sec:seq}
+
+\begin{center}
+    \captionof{table}{Input files}
+    \label{tab:annotfiles}
+    \begin{longtable}{ l l p{0.4\textwidth} }
+            \hline
+            File & Checksum & Name\\
+            \hline \hline
+        \endhead
+            \hline
+            \multicolumn{3}{c}{\textit{Continued on next page}}\\
+            \hline
+        \endfoot
+            \hline
+        \endlastfoot
+        Read 1 file & ((( lib.flexiprep_files.input_R1.md5|truncate(7, True, "") ))) & ((( lib.flexiprep_files.input_R1.path|basename )))\\
+        ((* if lib.flexiprep_files.input_R2 *))
+        Read 2 file & ((( lib.flexiprep_files.input_R2.md5|truncate(7, True, "") ))) & ((( lib.flexiprep_files.input_R2.path|basename )))\\
+        ((* endif *))
+    \end{longtable}
+\end{center}
+% HACK: to keep table counters in sync
+\addtocounter{table}{-1}
+
 ((* include "lib_seqeval.tex" *))
 \clearpage
 ((* include "lib_mapping.tex" *))