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SVdetection
popsim
Commits
3d75a068
Commit
3d75a068
authored
8 years ago
by
Floreal Cabanettes
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Add res dir to build_jflow_command_line script
parent
80c40cc4
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build_jflow_command_line.py
+3
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build_jflow_command_line.py
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1 deletion
build_jflow_command_line.py
+
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1
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3d75a068
...
...
@@ -6,6 +6,7 @@ parser = argparse.ArgumentParser(description='Generate simulated populations wit
parser
.
add_argument
(
"
--nb-inds
"
,
help
=
"
Number of individuals to generate
"
,
required
=
True
)
parser
.
add_argument
(
"
--reference
"
,
help
=
"
Reference genome
"
,
required
=
True
)
parser
.
add_argument
(
"
--prepare
"
,
help
=
"
Prepare workflow (default is detection workflow)
"
,
action
=
'
store_const
'
,
const
=
True
,
default
=
False
)
parser
.
add_argument
(
"
--res-dir
"
,
help
=
"
Results dirs containing fastq reads files
"
,
default
=
"
res
"
)
parser
.
add_argument
(
"
--chromosomes
"
,
help
=
"
Chromosomes list, comma separated
"
,
default
=
False
)
parser
.
add_argument
(
"
--params
"
,
help
=
"
Other parameters for the workflow
"
,
default
=
False
)
parser
.
add_argument
(
"
--bams-dir
"
,
help
=
"
Directory containing bams for each individual, created by cnvprepare
"
,
default
=
False
)
...
...
@@ -36,7 +37,8 @@ cmd += "--reference-genome " + reference
if
args
.
prepare
:
for
i
in
range
(
1
,
int
(
nb_inds
)
+
1
):
cmd
+=
"
--sample name=
\"
INDIV_{0}
\"
reads-1=
\"
res/INDIV_{0}_100_180_1.fq.gz
\"
reads-2=
\"
res/INDIV_{0}_100_180_2.fq.gz
\"
"
.
format
(
i
)
cmd
+=
"
--sample name=
\"
INDIV_{0}
\"
reads-1=
\"
"
+
args
.
res_dir
+
"
/INDIV_{0}_100_180_1.fq.gz
\"
reads-2=
\"
"
+
\
args
.
res_dir
+
"
/INDIV_{0}_100_180_2.fq.gz
\"
"
.
format
(
i
)
else
:
for
i
in
range
(
1
,
int
(
nb_inds
)
+
1
):
cmd
+=
"
--sample name=
\"
INDIV_{0}
\"
alignments=
\"
{1}/INDIV_{0}-sorted-md.bam
\"
"
.
format
(
i
,
bams_dir
)
...
...
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