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biopet.biopet
Commits
5db19c93
Commit
5db19c93
authored
Mar 09, 2015
by
bow
Browse files
Report update
parent
14d8d45f
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 @
5db19c93
...
@@ -403,6 +403,7 @@ class GentrapLib(object):
...
@@ -403,6 +403,7 @@ class GentrapLib(object):
self
.
_raw
=
summary
self
.
_raw
=
summary
# flexiprep settings
# flexiprep settings
self
.
flexiprep
=
summary
.
get
(
"flexiprep"
,
{})
self
.
flexiprep
=
summary
.
get
(
"flexiprep"
,
{})
self
.
flexiprep_files
=
summary
.
get
(
"flexiprep"
,
{}).
get
(
"files"
,
{}).
get
(
"pipeline"
,
{})
self
.
clipping
=
not
self
.
flexiprep
[
"settings"
][
"skip_clip"
]
self
.
clipping
=
not
self
.
flexiprep
[
"settings"
][
"skip_clip"
]
self
.
trimming
=
not
self
.
flexiprep
[
"settings"
][
"skip_trim"
]
self
.
trimming
=
not
self
.
flexiprep
[
"settings"
][
"skip_trim"
]
self
.
is_paired_end
=
self
.
flexiprep
[
"settings"
][
"paired"
]
self
.
is_paired_end
=
self
.
flexiprep
[
"settings"
][
"paired"
]
...
...
public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/lib.tex
View file @
5db19c93
\section
{
Library "((( lib.name )))" Results
}
\section
{
Library "((( lib.name )))" Results
}
\label
{
lib:(((lib.name)))
}
\label
{
lib:(((lib.name)))
}
\subsection
{
Input information
}
\label
{
sec:seq
}
\begin{center}
\captionof
{
table
}{
Input files
}
\label
{
tab:annotfiles
}
\begin{longtable}
{
l l p
{
0.4
\textwidth
}
}
\hline
File
&
Checksum
&
Name
\\
\hline
\hline
\endhead
\hline
\multicolumn
{
3
}{
c
}{
\textit
{
Continued on next page
}}
\\
\hline
\endfoot
\hline
\endlastfoot
Read 1 file
&
((( lib.flexiprep
_
files.input
_
R1.md5|truncate(7, True, "") )))
&
((( lib.flexiprep
_
files.input
_
R1.path|basename )))
\\
((* if lib.flexiprep
_
files.input
_
R2 *))
Read 2 file
&
((( lib.flexiprep
_
files.input
_
R2.md5|truncate(7, True, "") )))
&
((( lib.flexiprep
_
files.input
_
R2.path|basename )))
\\
((* endif *))
\end{longtable}
\end{center}
% HACK: to keep table counters in sync
\addtocounter
{
table
}{
-1
}
((* include "lib
_
seqeval.tex" *))
((* include "lib
_
seqeval.tex" *))
\clearpage
\clearpage
((* include "lib
_
mapping.tex" *))
((* include "lib
_
mapping.tex" *))
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