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Maintenance - Mise à jour mensuelle Lundi 6 Février entre 7h00 et 9h00
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genotoul-bioinfo
ng6
Commits
2e206f29
Commit
2e206f29
authored
Jul 01, 2014
by
Claire Kuchly
Browse files
multiple fastq for one sample
parent
725b1b00
Changes
1
Hide whitespace changes
Inline
Side-by-side
workflows/illumina_diversity_qc/__init__.py
View file @
2e206f29
...
...
@@ -96,6 +96,9 @@ class IlluminaDiversityQC (NG6Workflow):
concatenatefastq
=
self
.
add_component
(
"ConcatenateFilesGroups"
,
[
saved_files
,
reads_prefixes
])
saved_files
=
concatenatefastq
.
concat_files
addrawfiles
=
self
.
add_component
(
"AddRawFiles"
,
[
self
.
runobj
,
saved_files
,
self
.
args
[
"compression"
]])
concatenate1
=
self
.
add_component
(
"ConcatenateFilesGroups"
,
[
filtered_read1_files
,
(
Utils
.
get_group_basenames
(
self
.
read1_files
,
"read"
)).
keys
()],
component_prefix
=
"read1"
)
concatenate2
=
self
.
add_component
(
"ConcatenateFilesGroups"
,
[
filtered_read2_files
,
(
Utils
.
get_group_basenames
(
self
.
read2_files
,
"read"
)).
keys
()],
component_prefix
=
"read2"
)
# make some statistics on raw file
fastqc
=
self
.
add_component
(
"FastQC"
,
[
filtered_read1_files
+
filtered_read2_files
,
(
group_prefix
is
not
None
),
True
,
run_name
+
"_fastqc.tar.gz"
],
parent
=
fastqilluminafilter
)
...
...
@@ -104,10 +107,10 @@ class IlluminaDiversityQC (NG6Workflow):
try
:
self
.
args
[
"databank"
].
extend
([
self
.
get_resource
(
"phix_bwa"
),
self
.
get_resource
(
"ecoli_bwa"
),
self
.
get_resource
(
"yeast_bwa"
)])
except
:
pass
if
self
.
args
[
"databank"
]:
contamination_search
=
self
.
add_component
(
"ContaminationSearch"
,
[
filtered_read1_files
+
filtered_read2_files
,
self
.
args
[
"databank"
],
reads_prefixes
],
parent
=
fastqilluminafilter
)
contamination_search
=
self
.
add_component
(
"ContaminationSearch"
,
[
filtered_read1_files
+
filtered_read2_files
,
self
.
args
[
"databank"
],
reads_prefixes
],
parent
=
fastqilluminafilter
)
# merge overlapping pair
join_pairs
=
self
.
add_component
(
"Flash"
,
[
filtered_read1_files
,
filtered_read2
_files
,
self
.
args
[
"mismatch_ratio"
],
self
.
args
[
"min_overlap"
],
self
.
args
[
"max_overlap"
]],
parent
=
fastqilluminafilter
)
join_pairs
=
self
.
add_component
(
"Flash"
,
[
concatenate1
.
concat_files
,
concatenate2
.
concat
_files
,
self
.
args
[
"mismatch_ratio"
],
self
.
args
[
"min_overlap"
],
self
.
args
[
"max_overlap"
]],
parent
=
fastqilluminafilter
)
if
self
.
args
[
"assignation_databank"
]
is
not
None
:
# subset assignation
...
...
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