Commit 5db19c93 authored by bow's avatar bow
Browse files

Report update

parent 14d8d45f
...@@ -403,6 +403,7 @@ class GentrapLib(object): ...@@ -403,6 +403,7 @@ class GentrapLib(object):
self._raw = summary self._raw = summary
# flexiprep settings # flexiprep settings
self.flexiprep = summary.get("flexiprep", {}) self.flexiprep = summary.get("flexiprep", {})
self.flexiprep_files = summary.get("flexiprep", {}).get("files", {}).get("pipeline", {})
self.clipping = not self.flexiprep["settings"]["skip_clip"] self.clipping = not self.flexiprep["settings"]["skip_clip"]
self.trimming = not self.flexiprep["settings"]["skip_trim"] self.trimming = not self.flexiprep["settings"]["skip_trim"]
self.is_paired_end = self.flexiprep["settings"]["paired"] self.is_paired_end = self.flexiprep["settings"]["paired"]
......
\section{Library "((( lib.name )))" Results} \section{Library "((( lib.name )))" Results}
\label{lib:(((lib.name)))} \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" *)) ((* include "lib_seqeval.tex" *))
\clearpage \clearpage
((* include "lib_mapping.tex" *)) ((* include "lib_mapping.tex" *))
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