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genotoul-bioinfo
jflow
Commits
848fd892
Commit
848fd892
authored
Sep 25, 2014
by
Jerome Mariette
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parent
397f3cb0
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1
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workflows/alignment/__init__.py
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848fd892
...
...
@@ -25,12 +25,10 @@ class Alignment (Workflow):
return
"Align reads against a reference genome"
def
define_parameters
(
self
,
function
=
"process"
):
self
.
add_input_file_list
(
"read_1"
,
"Which read1 files should be used"
,
type
=
"browsefile"
,
file_format
=
"fastq"
,
required
=
True
)
self
.
add_input_file_list
(
"read_1"
,
"Which read1 files should be used"
,
file_format
=
"fastq"
,
required
=
True
)
self
.
add_input_file_list
(
"read_2"
,
"Which read2 files should be used (if single end, leave empty)"
,
file_format
=
"fastq"
)
self
.
add_input_file
(
"reference_genome"
,
"Which genome should the read being align on"
,
required
=
True
,
file_format
=
"fasta"
)
self
.
add_parameter
(
"test"
,
"Whin"
,
type
=
"bool"
)
def
process
(
self
):
# index the reference genome
bwaindex
=
self
.
add_component
(
"BWAIndex"
,
[
self
.
reference_genome
])
...
...
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