Skip to content
GitLab
Menu
Projects
Groups
Snippets
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
genotoul-bioinfo
ng6
Commits
16503d88
Commit
16503d88
authored
Nov 13, 2019
by
Romain Therville
🐭
Browse files
Merge branch '#139_debug' into 'master'
#139
debug See merge request
!63
parents
4b72adb5
926392ab
Changes
1
Hide whitespace changes
Inline
Side-by-side
src/ng6/ng6workflow.py
View file @
16503d88
...
...
@@ -190,9 +190,6 @@ class NG6Workflow (BasicNG6Workflow):
pidx
=
1
nidx
=
1
for
rang
,
sample
in
enumerate
(
self
.
samples
)
:
print
(
sample
)
print
(
"sample readsi"
)
print
(
sample
.
readsi
)
if
sample
.
name
:
self
.
samples_names
.
append
(
sample
.
name
)
else
:
...
...
@@ -686,15 +683,15 @@ class CasavaNG6Workflow(NG6Workflow):
# archive the files
#TODO : if self.group_prefix == None, the create the output of fastqilluminafilter in the run.get_work_directory()
saved_files
=
filtered_read1_files
+
filtered_read2_files
+
self
.
get_all_reads
(
"readsi"
)
saved_files
=
filtered_read1_files
+
filtered_read2_files
+
self
.
get_all_reads
(
"index"
)
logging
.
getLogger
(
"CasavaNG6Workflow"
).
debug
(
"illumina_process saved_files = "
+
","
.
join
(
saved_files
))
reads_prefixes
=
None
if
self
.
group_prefix
!=
None
:
# concatenate fastq
reads_prefixes
=
list
((
Utils
.
get_group_basenames
(
saved_files
,
"read"
)).
keys
())
logging
.
getLogger
(
"CasavaNG6Workflow"
).
debug
(
"illumina_process reads_prefixes = "
+
","
.
join
(
reads_prefixes
))
logging
.
getLogger
(
"CasavaNG6Workflow"
).
debug
(
"illumina_process saved_files = "
+
","
.
join
(
saved_files
))
concatenatefastq
=
self
.
add_component
(
"ConcatenateFilesGroups"
,
[
self
.
runobj
,
saved_files
,
reads_prefixes
])
concatenatefastq
=
self
.
add_component
(
"ConcatenateFilesGroups"
,
[
self
.
runobj
,
saved_files
,
reads_prefixes
])
saved_files
=
concatenatefastq
.
concat_files
logging
.
getLogger
(
"CasavaNG6Workflow"
).
debug
(
"illumina_process after concatenatefastq, saved_files = "
+
","
.
join
(
saved_files
))
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a 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