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biopet.biopet
Commits
b71ac0fe
Commit
b71ac0fe
authored
Mar 09, 2015
by
bow
Browse files
Add initial version table to report[C
parent
133cd485
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/pdf_report.py
View file @
b71ac0fe
...
...
@@ -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__
,
...
...
public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/main.tex
View file @
b71ac0fe
...
...
@@ -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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