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Statistical-Genetics
JASS_suite_pipeline
Commits
97d21fae
Commit
97d21fae
authored
2 years ago
by
Hanna JULIENNE
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removed glob pattern in preambule
parent
c08fac16
Branches
jacques
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v12.6.0
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jass_pipeline.nf
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View file @
97d21fae
...
@@ -51,8 +51,8 @@ Region_channel = Channel.fromPath(params.region)
...
@@ -51,8 +51,8 @@ Region_channel = Channel.fromPath(params.region)
Region_channel2
=
Channel
.
fromPath
(
params
.
region
)
Region_channel2
=
Channel
.
fromPath
(
params
.
region
)
chr_channel
=
Channel
.
from
(
1
..
22
)
chr_channel
=
Channel
.
from
(
1
..
22
)
ref_chr_
channel
=
Channel
.
fromP
ath
(
params
.
ref_panel
+
"/ALL_ensemble_1000G_hg38_EAS_chr*.bim"
)
ref_chr_
p
ath
=
params
.
ref_panel
+
"/ALL_ensemble_1000G_hg38_EAS_chr*.bim"
ld_channel
=
Channel
.
fromPath
(
params
.
ld_folder
)
extract_sample_size_script_channel
=
Channel
.
fromPath
(
"${projectDir}/bin/extract_sample_size.py"
)
extract_sample_size_script_channel
=
Channel
.
fromPath
(
"${projectDir}/bin/extract_sample_size.py"
)
generate_trait_pairs_channel
=
Channel
.
fromPath
(
"${projectDir}/bin/generate_trait_pairs.py"
)
generate_trait_pairs_channel
=
Channel
.
fromPath
(
"${projectDir}/bin/generate_trait_pairs.py"
)
...
@@ -108,8 +108,8 @@ process Impute_GWAS {
...
@@ -108,8 +108,8 @@ process Impute_GWAS {
publishDir
"${params.output_folder}"
,
pattern:
"imputed_GWAS/*.txt"
,
mode:
'copy'
publishDir
"${params.output_folder}"
,
pattern:
"imputed_GWAS/*.txt"
,
mode:
'copy'
input:
input:
path
gwas_files
from
cleaned_gwas_chr_channel
path
gwas_files
from
cleaned_gwas_chr_channel
path
ref_file
from
ref_chr_
channel
.
collect
()
path
ref_file
from
Channel
.
fromPath
(
ref_chr_
path
)
.
collect
()
path
ld_file
from
ld_c
hannel
.
collect
()
path
ld_file
from
C
hannel
.
fromPath
(
param
.
ld_folder
).
collect
()
output:
output:
path
"imputed_GWAS/*.txt"
into
imputed_gwas_channel
path
"imputed_GWAS/*.txt"
into
imputed_gwas_channel
path
"imputed_GWAS/*.txt"
into
imputed_gwas_channel2
path
"imputed_GWAS/*.txt"
into
imputed_gwas_channel2
...
...
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