Commit b71ac0fe authored by bow's avatar bow
Browse files

Add initial version table to report[C

parent 133cd485
......@@ -510,9 +510,29 @@ class GentrapRun(object):
for s in self.sample_names}
self.files = summary["gentrap"]["files"]
self.executables = summary["gentrap"]["executables"]
self.settings = summary["gentrap"]["settings"]
self.version = self.settings["version"]
# list containing all exes
self.all_executables = summary["gentrap"]["executables"]
# list containing exes we want to display
executables = [
("cutadapt", "adapter clipping"),
("sickle", "base quality trimming"),
("fastqc", "sequence metrics collection"),
("gsnap", "alignment"),
("htseqcount", "fragment counting"),
self.executables = {k: self.all_executables[k] for k, _ in executables}
for exe, desc in executables:
self.executables[exe]["desc"] = desc
# since we get the version from the tools we use
if self.all_executables.get("collectalignmentsummarymetrics") is not None:
self.executables["picard"] = self.all_executables["collectalignmentsummarymetrics"]
self.executables["picard"]["desc"] = "alignment_metrics_collection"
# since we get the version from the sub tools we use
if self.all_executables.get("samtoolsview") is not None:
self.executables["samtools"] = self.all_executables["samtoolsview"]
self.executables["samtools"]["desc"] = "various post-alignment processing"
def __repr__(self):
return "{0}(\"{1}\")".format(self.__class__.__name__,
......@@ -66,7 +66,32 @@
This document outlines the results obtained from running Gentrap, a generic
pipeline for transcriptome analysis.
pipeline for transcriptome analysis. The pipeline itself is composed of several
programs, listed in Table~\ref{tab:programs}. Note that the list only contains
the programs used in this pipeline run.
\captionof{table}{Programs in Gentrap}
\begin{longtable}{ l l l p{0.2\textwidth} }
Program & Version & Checksum & Usage\\
\hline \hline
\multicolumn{3}{c}{\textit{Continued on next page}}\\
Gentrap & ((( run.version ))) & - & the full pipeline\\
((* for program, info in run.executables.items()|sort *))
((( program ))) & ((( info.version ))) & ((( info.md5|truncate(7, True, "") ))) & ((( info.desc )))\\
((* endfor *))
% HACK: to keep table counters in sync
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