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biopet.biopet
Commits
41883883
Commit
41883883
authored
Mar 07, 2015
by
bow
Browse files
Add all fastqc plots to report
parent
3c2f3b45
Changes
2
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public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/pdf_report.py
View file @
41883883
...
...
@@ -389,21 +389,17 @@ class GentrapLib(object):
self
.
trimming
=
not
self
.
flexiprep
[
"settings"
][
"skip_trim"
]
self
.
is_paired_end
=
self
.
flexiprep
[
"settings"
][
"paired"
]
if
"fastqc_R1"
in
self
.
flexiprep
[
"files"
]:
self
.
fastqc_r1
=
FastQC
(
self
.
flexiprep
[
"files"
][
"fastqc_R1"
][
"fastqc_data"
][
"path"
])
else
:
self
.
fastqc_r1
=
None
self
.
fastqc_r1_files
=
self
.
flexiprep
[
"files"
][
"fastqc_R1"
]
self
.
fastqc_r1
=
FastQC
(
self
.
fastqc_r1_files
[
"fastqc_data"
][
"path"
])
if
"fastqc_R2"
in
self
.
flexiprep
[
"files"
]:
self
.
fastqc_r2
=
FastQC
(
self
.
flexiprep
[
"files"
][
"fastqc_R2"
][
"fastqc_data"
][
"path"
])
else
:
self
.
fastqc_r2
=
None
self
.
fastqc_r2_files
=
self
.
flexiprep
[
"files"
][
"fastqc_R2"
]
self
.
fastqc_r2
=
FastQC
(
self
.
fastqc_r2_files
[
"fastqc_data"
][
"path"
])
if
"fastqc_R1_qc"
in
self
.
flexiprep
[
"files"
]:
self
.
fastqc_r1_qc
=
FastQC
(
self
.
flexiprep
[
"files"
][
"fastqc_R1_qc"
][
"fastqc_data"
][
"path"
])
else
:
self
.
fastqc_r1_qc
=
None
self
.
fastqc_r1_qc_files
=
self
.
flexiprep
[
"files"
][
"fastqc_R1_qc"
]
self
.
fastqc_r1_qc
=
FastQC
(
self
.
fastqc_r1_qc_files
[
"fastqc_data"
][
"path"
])
if
"fastqc_R2_qc"
in
self
.
flexiprep
[
"files"
]:
self
.
fastqc_r2_qc
=
FastQC
(
self
.
flexiprep
[
"files"
][
"fastqc_R2_qc"
][
"fastqc_data"
][
"path"
])
else
:
self
.
fastqc_r2_qc
=
None
self
.
fastqc_r2_qc_files
=
self
.
flexiprep
[
"files"
][
"fastqc_R2_qc"
]
self
.
fastqc_r2_qc
=
FastQC
(
self
.
fastqc_r2_qc_files
[
"fastqc_data"
][
"path"
])
def
__repr__
(
self
):
return
"{0}(sample=
\"
{1}
\"
, lib=
\"
{2}
\"
)"
.
format
(
...
...
public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/lib_seqeval.tex
View file @
41883883
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