Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
J
JASS_suite_pipeline
Manage
Activity
Members
Labels
Plan
Wiki
Code
Merge requests
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Snippets
Build
Pipelines
Jobs
Pipeline schedules
Artifacts
Deploy
Releases
Container registry
Model registry
Operate
Environments
Analyze
Value stream analytics
Contributor analytics
CI/CD analytics
Repository analytics
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
Statistical-Genetics
JASS_suite_pipeline
Commits
e214a50d
Commit
e214a50d
authored
2 years ago
by
Hanna JULIENNE
Browse files
Options
Downloads
Patches
Plain Diff
resolve conflict in pipeline
parent
b6acf71b
Branches
Branches containing commit
No related tags found
1 merge request
!2
Pipeline ancestry
Changes
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
jass_pipeline.nf
+0
-12
0 additions, 12 deletions
jass_pipeline.nf
with
0 additions
and
12 deletions
jass_pipeline.nf
+
0
−
12
View file @
e214a50d
...
...
@@ -16,13 +16,9 @@ params.meta_data = "${projectDir}"+"/input_files/Data_test_EAS.csv" // file desc
params
.
gwas_folder
=
"${projectDir}"
+
'/test_data/hg38_EAS/'
params
.
ref_panel
=
'/pasteur/zeus/projets/p02/GGS_JASS/jass_analysis_pipeline/Ref_panel_by_chr/'
params
.
region
=
"${projectDir}"
+
"/input_files/All_Regions_ALL_ensemble_1000G_hg38_EAS.bed"
<<<<<<<
HEAD
param
.
ref_panel_wg_channel
=
"${projectDir}"
+
"/Ref_Panel/1000G_EAS_0_01_chr22_21.csv"
=======
params
.
ref_panel_WG
=
"${projectDir}"
+
"/Ref_Panel/1000G_EAS_0_01_chr22_21.csv"
//"${projectDir}/Ref_Panel/1000G_EAS_0_01_chr22.csv"
>>>>>>>
1
e9f87b9950df3c765cf738e14fac767e4ecba8a
params
.
ancestry
=
"EAS"
params
.
prefix
=
"ALL_ensemble_1000G_hg38_EAS_chr"
params
.
prefix_Impute_GWAS
=
"ALL_ensemble_1000G_hg38_EAS_"
...
...
@@ -58,10 +54,6 @@ chr_channel = Channel.from(1..22)
ref_chr_channel
=
Channel
.
fromPath
(
params
.
ref_panel
+
"/ALL_ensemble_1000G_hg38_EAS_chr*.bim"
)
ld_channel
=
Channel
.
fromPath
(
"/pasteur/zeus/projets/p02/GGS_WKD/DATA_1000G/Panels/Matrix_LD_RAISS/EAS/*.ld"
)
<<<<<<<
HEAD
//"${projectDir}/Ref_Panel/1000G_EAS_0_01_chr22.csv"
=======
>>>>>>>
1
e9f87b9950df3c765cf738e14fac767e4ecba8a
extract_sample_size_script_channel
=
Channel
.
fromPath
(
"${projectDir}/bin/extract_sample_size.py"
)
generate_trait_pairs_channel
=
Channel
.
fromPath
(
"${projectDir}/bin/generate_trait_pairs.py"
)
parse_correlation_channel
=
Channel
.
fromPath
(
"${projectDir}/bin/parse_correlation_results.py"
)
...
...
@@ -86,11 +78,7 @@ process Clean_GWAS {
publishDir
"${params.output_folder}/harmonized_GWAS_files/"
,
pattern:
"*.txt"
,
mode:
'copy'
publishDir
"${params.output_folder}"
,
pattern:
"harmonized_GWAS_1_file/*.txt"
,
mode:
'copy'
input:
<<<<<<<
HEAD
path
ref_panel
from
params
.
ref_panel_wg_channel
=======
path
ref_panel
from
params
.
ref_panel_WG
>>>>>>>
1
e9f87b9950df3c765cf738e14fac767e4ecba8a
path
meta_chunk
from
meta_data
output:
path
"harmonized_GWAS_1_file/*.txt"
into
cleaned_gwas_channel
...
...
This diff is collapsed.
Click to expand it.
Preview
0%
Loading
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment