Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Holland Computing Center
chipathlon
Commits
ea23018f
Commit
ea23018f
authored
Mar 14, 2016
by
aknecht2
Browse files
Updated bwa additional files. Adjusted file naming in genome checking.
parent
8f82cd13
Changes
2
Hide whitespace changes
Inline
Side-by-side
chipathlon/conf.py
View file @
ea23018f
...
...
@@ -17,7 +17,7 @@ file_extensions = {
"sam"
:
[
"sam"
],
"bam"
:
[
"bam"
],
"bed"
:
[
"bed"
,
"narrowPeak"
,
"broadPeak"
],
"bwa_genome"
:
[
"amb"
,
"ann"
,
"bwt"
,
"pac"
,
"sa
c
"
],
"bwa_genome"
:
[
"amb"
,
"ann"
,
"bwt"
,
"pac"
,
"sa"
],
"bowtie2_genome"
:
[
"1.bt2"
,
"2.bt2"
,
"3.bt2"
,
"4.bt2"
,
"rev.1.bt2"
,
"rev.2.bt2"
]
}
...
...
chipathlon/workflow.py
View file @
ea23018f
...
...
@@ -172,13 +172,13 @@ class Workflow(object):
if
not
os
.
path
.
isfile
(
prefix
+
"."
+
ext
)
and
not
os
.
path
.
isfile
(
base_file
+
"."
+
ext
):
missing
.
append
(
ext
)
else
:
f
=
File
(
gen_prefix
+
"."
+
ext
)
f
new
=
File
(
gen_prefix
+
"."
+
ext
)
if
os
.
path
.
isfile
(
prefix
+
"."
+
ext
):
f
.
addPFN
(
prefix
+
"."
+
ext
)
f
new
.
addPFN
(
prefix
+
"."
+
ext
)
else
:
f
.
addPFN
(
base_file
+
"."
+
ext
)
self
.
files
[
gen_prefix
+
"."
+
ext
]
=
f
self
.
dax
.
addFile
(
f
)
f
new
.
addPFN
(
base_file
+
"."
+
ext
)
self
.
files
[
gen_prefix
+
"."
+
ext
]
=
f
new
self
.
dax
.
addFile
(
f
new
)
if
len
(
missing
)
>
0
:
self
.
err
+=
"Genome defined with tool '%s' and assembly '%s' is missing additional_files with extensions %s.
\n
"
%
(
run
[
"align"
],
assembly
,
missing
)
else
:
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment