Commit 5434cd5c authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Merge branch 'fix_gentrap_report_pdf' into 'develop'

Fix gentrap report pdf



See merge request !266
parents 5da74ac4 239b74f8
......@@ -72,9 +72,9 @@ More information about clipping using cutadapt is available on the
Read 1 & ((( lib.flexiprep.stats.clipping_R1.num_reads_affected|nice_int )))
((* for adapter, stat in lib.flexiprep.stats.clipping_R1.adapters.iteritems() *))
((* if loop.first *))
& ((( adapter ))) & ((( stat[1]|nice_int )))\\
& ((( adapter ))) & ((( stat|nice_int )))\\
((* else *))
& & ((( adapter ))) & ((( stat[1]|nice_int )))\\
& & ((( adapter ))) & ((( stat|nice_int )))\\
((* endif *))
((* endfor *))
((* else *))
......@@ -85,9 +85,9 @@ More information about clipping using cutadapt is available on the
Read 2 & ((( lib.flexiprep.stats.clipping_R2.num_reads_affected|nice_int )))
((* for adapter, stat in lib.flexiprep.stats.clipping_R2.adapters.iteritems() *))
((* if loop.first *))
& ((( adapter ))) & ((( stat[1]|nice_int )))\\
& ((( adapter ))) & ((( stat|nice_int )))\\
((* else *))
& & ((( adapter ))) & ((( stat[1]|nice_int )))\\
& & ((( adapter ))) & ((( stat|nice_int )))\\
((* endif *))
((* endfor *))
((* else *))
......@@ -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}
......@@ -141,12 +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.num_reads_discarded_R1|nice_int )))\\
Discarded FASTQ records from read 2 & ((( lib.flexiprep.stats.trimming.num_reads_discarded_R2|nice_int )))\\
\hline
Discarded FASTQ records from both reads & ((( lib.flexiprep.stats.trimming.num_reads_discarded_both|nice_int )))\\
\hline
Total kept FASTQ reads & ((( lib.flexiprep.stats.trimming.num_reads_kept|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}
......
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