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genotoul-bioinfo
ng6
Commits
653760d4
Commit
653760d4
authored
Jan 30, 2019
by
mmanno
Browse files
Change path to scripts R
parent
278939c7
Changes
2
Hide whitespace changes
Inline
Side-by-side
src/ng6/utils.py
View file @
653760d4
...
...
@@ -300,7 +300,7 @@ class Utils(object):
"""
group_basenames
=
{}
for
file
in
file_list
:
for
file
in
file_list
:
file_name_fields
=
os
.
path
.
basename
(
file
).
split
(
Utils
.
CASAVA_FILENAME_SEPARATOR
)
group_tag
=
Utils
.
CASAVA_FILENAME_SEPARATOR
.
join
(
file_name_fields
[:
Utils
.
CASAVA_FILENAME
[
group_by
]]
)
...
...
@@ -309,7 +309,7 @@ class Utils(object):
group_basenames
[
group_tag
].
append
(
file
)
else
:
group_basenames
[
group_tag
]
=
[
file
]
logging
.
getLogger
(
"Utils"
).
debug
(
"get_group_basenames. group_basenames = "
+
","
.
join
(
group_basenames
))
return
group_basenames
@
staticmethod
...
...
workflows/ont_qc/components/run_stats.py
View file @
653760d4
...
...
@@ -227,14 +227,14 @@ class Run_stats (Analysis):
#print (self.sequencing_summary_file)
self
.
add_shell_execution
(
self
.
get_exec_path
(
"Rscript"
)
+
" /
work/ng6-test/claire/test_ont_qc
/graph_albacoresummary.R "
+
' -f '
+
'$1'
+
' --out '
+
self
.
output_directory
+
" 2> "
+
' $2'
,
self
.
add_shell_execution
(
self
.
get_exec_path
(
"Rscript"
)
+
" /
save/sbsuser/scripts-ngs/current/ont
/graph_albacoresummary.R "
+
' -f '
+
'$1'
+
' --out '
+
self
.
output_directory
+
" 2> "
+
' $2'
,
cmd_format
=
'{EXE} {IN} {OUT}'
,
map
=
False
,
inputs
=
self
.
sequencing_summary_file
,
outputs
=
self
.
stderr
)
if
self
.
barcoded
==
"yes"
:
self
.
add_shell_execution
(
self
.
get_exec_path
(
"Rscript"
)
+
" /
work/ng6-test/claire/test_ont_qc
/graph_albacoresummary_barcode.R "
+
' -f '
+
'$1'
+
' --out '
+
self
.
output_directory
+
" 2> "
+
' $2'
,
self
.
add_shell_execution
(
self
.
get_exec_path
(
"Rscript"
)
+
" /
save/sbsuser/scripts-ngs/current/ont
/graph_albacoresummary_barcode.R "
+
' -f '
+
'$1'
+
' --out '
+
self
.
output_directory
+
" 2> "
+
' $2'
,
cmd_format
=
'{EXE} {IN} {OUT}'
,
map
=
False
,
inputs
=
self
.
sequencing_summary_file
,
...
...
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