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genotoul-bioinfo
ng6
Commits
a41a3010
Commit
a41a3010
authored
Feb 07, 2019
by
Maxime Manno
🍜
Browse files
Add option to enable or disable trimming
parent
653760d4
Changes
1
Hide whitespace changes
Inline
Side-by-side
workflows/ont_qc/__init__.py
View file @
a41a3010
...
...
@@ -30,6 +30,7 @@ class OntQualityCheck (NG6Workflow):
def
define_parameters
(
self
,
function
=
"process"
):
logging
.
getLogger
(
"jflow"
).
debug
(
"Begin OntQualityCheck.define_parameters! ont_qc"
)
self
.
add_parameter
(
"compression"
,
"How should the data be compressed once archived"
,
choices
=
[
"none"
,
"gz"
,
"bz2"
],
default
=
"gz"
)
self
.
add_parameter
(
"trimming"
,
"use trimming with porechop or not"
,
choices
=
[
"yes"
,
"no"
],
default
=
"yes"
)
self
.
add_parameter
(
"nb_threads"
,
"Number of threads to use for porechop (default=16)."
,
default
=
16
)
self
.
add_parameter
(
"fileformat"
,
"The file format for porechop (default=fastq)."
,
choices
=
[
"fastq"
,
"fasta"
],
default
=
"fastq"
)
self
.
add_input_file
(
"summary_file"
,
"Input summary basecalling file"
,
default
=
None
)
...
...
@@ -52,7 +53,8 @@ class OntQualityCheck (NG6Workflow):
addrawfiles
=
self
.
add_component
(
"AddRawFiles"
,
[
self
.
runobj
,
self
.
get_all_reads
(),
self
.
compression
])
#nanoplot = self.add_component("Nanoplot", [sample.name,self.get_all_reads(), self.nb_threads, True, "png", self.nanoplot_color,"nanoplot.tar.gz"])
ontstat
=
self
.
add_component
(
"Run_stats"
,
[
self
.
summary_file
,
self
.
barcoded
])
trim_porechop
=
self
.
add_component
(
"Trim_porechop"
,
[
self
.
get_all_reads
(),
self
.
nb_threads
,
self
.
fileformat
,
"discard_middle"
])
if
self
.
trimming
==
"yes"
:
trim_porechop
=
self
.
add_component
(
"Trim_porechop"
,
[
self
.
get_all_reads
(),
self
.
nb_threads
,
self
.
fileformat
,
"discard_middle"
])
if
self
.
fast5dir
!=
None
:
fast5archive
=
self
.
add_component
(
"Fast5archive"
,
[
self
.
fast5dir
,
"fast5archive.tar"
])
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