From b71ac0fe8a5de253fa4f6c513c92b22e1399355e Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Mon, 9 Mar 2015 11:22:50 +0100
Subject: [PATCH] =?UTF-8?q?Add=20initial=20version=20table=20to=20report?=
=?UTF-8?q?=1B[C?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
---
.../pipelines/gentrap/scripts/pdf_report.py | 22 ++++++++++++++-
.../pipelines/gentrap/templates/pdf/main.tex | 27 ++++++++++++++++++-
2 files changed, 47 insertions(+), 2 deletions(-)
diff --git a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/pdf_report.py b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/pdf_report.py
index 9cdcaf951..455c142de 100755
--- a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/pdf_report.py
+++ b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/pdf_report.py
@@ -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__,
diff --git a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/main.tex b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/main.tex
index 0673d4c0d..a02acdd12 100644
--- a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/main.tex
+++ b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/main.tex
@@ -66,7 +66,32 @@
\label{sec:intro}
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.
+
+\begin{center}
+ \captionof{table}{Programs in Gentrap}
+ \label{tab:programs}
+ \begin{longtable}{ l l l p{0.2\textwidth} }
+ \hline
+ Program & Version & Checksum & Usage\\
+ \hline \hline
+ \endhead
+ \hline
+ \multicolumn{3}{c}{\textit{Continued on next page}}\\
+ \hline
+ \endfoot
+ \hline
+ \endlastfoot
+ 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 *))
+ \end{longtable}
+\end{center}
+% HACK: to keep table counters in sync
+\addtocounter{table}{-1}
\clearpage
--
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