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genotoul-bioinfo
ng6
Commits
32ba683d
Commit
32ba683d
authored
Oct 10, 2013
by
Penom Nom
Browse files
Clean component prefix for makecontig.
parent
70fd459f
Changes
1
Hide whitespace changes
Inline
Side-by-side
workflows/miseq_diversity/__init__.py
View file @
32ba683d
...
...
@@ -106,10 +106,10 @@ class MiSeqDiversity (NG6Workflow):
if
fileExtension
==
fileFormat
:
gunzip
=
self
.
add_component
(
"GunZipFiles"
,[
concat_read1_files
,
concat_read2_files
])
makecontigs
=
self
.
add_component
(
"MothurMakeContigs"
,
kwargs
=
{
'read1_files'
:
gunzip
.
fastq_R1
,
'read2_files'
:
gunzip
.
fastq_R2
,
\
'sample_name'
:
self
.
args
[
"sample_name"
],
'maxambig'
:
'0'
,
'maxlength'
:
self
.
args
[
"max_contigs_length"
]},
component_prefix
=
"
test
"
,
parent
=
fastqilluminafilter
)
'sample_name'
:
self
.
args
[
"sample_name"
],
'maxambig'
:
'0'
,
'maxlength'
:
self
.
args
[
"max_contigs_length"
]},
component_prefix
=
"
with_gz
"
,
parent
=
fastqilluminafilter
)
else
:
makecontigs
=
self
.
add_component
(
"MothurMakeContigs"
,
kwargs
=
{
'read1_files'
:
concat_read1_files
,
'read2_files'
:
concat_read2_files
,
\
'sample_name'
:
self
.
args
[
"sample_name"
],
'maxambig'
:
'0'
,
'maxlength'
:
self
.
args
[
"max_contigs_length"
]},
parent
=
fastqilluminafilter
)
'sample_name'
:
self
.
args
[
"sample_name"
],
'maxambig'
:
'0'
,
'maxlength'
:
self
.
args
[
"max_contigs_length"
]},
component_prefix
=
"without_gz"
,
parent
=
fastqilluminafilter
)
uniqueseqs
=
self
.
add_component
(
"MothurUniqueSeqs"
,
[
makecontigs
.
good_fasta_files
])
countseqs
=
self
.
add_component
(
"MothurCountSeqs"
,
[
uniqueseqs
.
unique_names_files
,
makecontigs
.
good_groups_files
])
pcrseqs
=
self
.
add_component
(
"MothurPcrSeqs"
,
kwargs
=
{
'fasta_files'
:
self
.
args
[
"reference_alignment"
],
'forward_primer'
:
self
.
args
[
"forward_primer"
],
\
...
...
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