num_reads_discarded changed into num_reads_discarded_total

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

@@ -99,26 +99,6 @@ More information about clipping using cutadapt is available on the
 \end{center}
 \addtocounter{table}{-1}
 
-((* if lib.is_paired_end *))
-After clipping, all read pairs are then checked ('synced') for their
-completeness. Read pairs whose other half has been discarded during
-clipping, will also be discarded. The summary of this step is available in
-Table~\ref{tab:clipsync}.
-
-\begin{center}
-    \captionof{table}{Summary of Post-Clipping Sync Step}
-    \label{tab:clipsync}
-    \begin{tabular}{ l  r }
-        \hline
-        Parameter & Count\\ \hline \hline
-        Discarded FASTQ records from read 1 & ((( lib.flexiprep.stats.fastq_sync.num_reads_discarded_R1|nice_int )))\\
-        Discarded FASTQ records from read 2 & ((( lib.flexiprep.stats.fastq_sync.num_reads_discarded_R2|nice_int )))\\
-        \hline
-        Total kept FASTQ records & ((( lib.flexiprep.stats.fastq_sync.num_reads_kept|nice_int )))\\
-        \hline
-    \end{tabular}
-\end{center}
-((* endif *))
 ((* endif *))
 
 \vspace{2mm}
@@ -141,8 +121,8 @@ Table~\ref{tab:clipsync}.
         \begin{tabular}{ l  r }
             \hline
             Parameter & Count\\ \hline \hline
-            Discarded FASTQ records from read 1 & ((( lib.flexiprep.stats.trimming_R1.num_reads_discarded|nice_int )))\\
-            Discarded FASTQ records from read 2 & ((( lib.flexiprep.stats.trimming_R2.num_reads_discarded|nice_int )))\\
+            Discarded FASTQ records from read 1 & ((( lib.flexiprep.stats.trimming_R1.num_reads_discarded_total|nice_int )))\\
+            Discarded FASTQ records from read 2 & ((( lib.flexiprep.stats.trimming_R2.num_reads_discarded_total|nice_int )))\\
             \hline
         \end{tabular}
     \end{center}