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JASS_suite_pipeline
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Hervé MENAGER
JASS_suite_pipeline
Commits
196d70d8
Commit
196d70d8
authored
Nov 28, 2019
by
hjulienne
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local example pipeline
parent
3c67f259
Changes
3
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3 changed files
with
31 additions
and
32 deletions
+31
-32
jass_pipeline.nf
jass_pipeline.nf
+3
-4
nextflow.config
nextflow.config
+15
-16
nextflow_slurm.config
nextflow_slurm.config
+13
-12
No files found.
jass_pipeline.nf
View file @
196d70d8
params.compute_project=true
params.compute_LDSC_matrix=true
params.compute_imputation=
tru
e
params.compute_imputation=
fals
e
params.meta_data = "${baseDir}"+"/input_files/test_
final
.csv"
params.gwas_folder = "
/pasteur/projets/policy01/PCMA/1._DATA/RAW.GWAS/
"
params.meta_data = "${baseDir}"+"/input_files/test_
meta
.csv"
params.gwas_folder = ""
params.ref_panel = '/pasteur/projets/policy01/PCMA/1._DATA/ImpG_refpanel/'
params.group = "${baseDir}/input_files/group.txt"
...
...
@@ -33,7 +33,6 @@ generate_trait_pairs_channel = Channel.fromPath("${baseDir}/generate_trait_pairs
parse_correlation_channel = Channel.fromPath("${baseDir}/parse_correlation_results.py")
process Compute_MAF{
input:
file ref_panel from ref_chr_channel3.collect()
...
...
nextflow.config
View file @
196d70d8
...
...
@@ -20,7 +20,7 @@ singularity {
}
process
{
executor
=
'
slurm
'
executor
=
'
local
'
maxErrors
=
10
maxRetries
=
3
maxForks
=
400
...
...
@@ -29,14 +29,13 @@ process{
cache
=
'deep'
withName
:
'Compute_MAF'
{
container
=
'plink_1.90b5--heea4ae3_0.sif
'
cpus
=
1
}
withName
:
'Compute_MAF'
{
container
=
'docker://quay.io/biocontainers/plink:1.90b5--heea4ae3_1
'
cpus
=
1
}
//
docker
://
quay
.
io
/
biocontainers
/
jass_preprocessing
:
1
.
0
--
py_0
withName
:
'create_WG_reference_panel'
{
container
=
'
jass_preprocessing_2.0--py_0.sif
'
container
=
'
docker://quay.io/biocontainers/jass_preprocessing:2.0.1--py_0
'
cpus
=
1
}
...
...
@@ -45,42 +44,42 @@ process{
}
withName
:
'Clean_GWAS'
{
//
container
=
'jass_preprocessing_2.0--py_0.sif
'
container
=
'docker://quay.io/biocontainers/jass_preprocessing:2.0.1--py_0
'
cpus
=
1
}
withName
:
'Impute_GWAS'
{
container
=
"
raiss_2.0--py_0.sif
"
container
=
"
docker://quay.io/biocontainers/raiss_2.0--py_0
"
cpus
=
1
}
withName
:
'Munge_LDSC_data'
{
container
=
'
ldsc_1.0.1--py_0.sif
'
container
=
'
docker://quay.io/biocontainers/ldsc_1.0.1--py_0
'
cpus
=
1
}
withName
:
'Generate_trait_pair'
{
container
=
'
jass_preprocessing_2.0--py_0.sif
'
container
=
'
docker://quay.io/biocontainers/jass_preprocessing_2.0.1--py_0
'
cpus
=
1
}
withName
:
'Correlation_LDSC_data'
{
container
=
"ldsc_1.0.1--py_0.sif"
container
=
"
docker://quay.io/biocontainers/
ldsc_1.0.1--py_0.sif"
cpus
=
1
}
withName
:
'Correlation_matrices'
{
container
=
'
jass_preprocessing_2.0--py_0.sif
'
container
=
'
docker://quay.io/biocontainers/jass_preprocessing_2.0.1--py_0
'
cpus
=
1
}
withName
:
'Create_inittable_LDSC'
{
container
=
'
jass_2.0--pyh5ca1d4c_0.sif
'
container
=
'
docker://quay.io/biocontainers/jass_2.0--pyh5ca1d4c_0
'
cpus
=
1
}
withName
:
'Create_inittable'
{
container
=
'
jass_2.0--pyh5ca1d4c_0.sif
'
container
=
'
docker://quay.io/biocontainers/jass_2.0--pyh5ca1d4c_0
'
cpus
=
1
}
...
...
@@ -89,7 +88,7 @@ process{
}
withName
:
'Create_project_data'
{
container
=
'
jass_2.0--pyh5ca1d4c_0.sif
'
container
=
'
docker://quay.io/biocontainers/jass_2.0--pyh5ca1d4c_0
'
cpus
=
1
}
...
...
nextflow_
local
.config
→
nextflow_
slurm
.config
View file @
196d70d8
...
...
@@ -25,17 +25,18 @@ process{
maxRetries
=
3
maxForks
=
400
queueSize
=
500
errorStrategy
=
'
retry
'
errorStrategy
=
'
finish
'
cache
=
'deep'
withName
:
'Compute_MAF'
{
container
=
'
docker://quay.io/biocontainers/plink_1.90b5--heea4ae3_0
'
container
=
'
plink_1.90b5--heea4ae3_0.sif
'
cpus
=
1
}
//
docker
://
quay
.
io
/
biocontainers
/
jass_preprocessing
:
1
.
0
--
py_0
withName
:
'create_WG_reference_panel'
{
container
=
'
docker://quay.io/biocontainers/jass_preprocessing:2.0.1--py_0
'
container
=
'
jass_preprocessing_2.0--py_0.sif
'
cpus
=
1
}
...
...
@@ -44,42 +45,42 @@ process{
}
withName
:
'Clean_GWAS'
{
container
=
'docker://quay.io/biocontainers/jass_preprocessing:2.0.1--py_0
'
//
container
=
'jass_preprocessing_2.0--py_0.sif
'
cpus
=
1
}
withName
:
'Impute_GWAS'
{
container
=
"
docker://quay.io/biocontainers/raiss_2.0--py_0
"
container
=
"
raiss_2.0--py_0.sif
"
cpus
=
1
}
withName
:
'Munge_LDSC_data'
{
container
=
'
docker://quay.io/biocontainers/ldsc_1.0.1--py_0
'
container
=
'
ldsc_1.0.1--py_0.sif
'
cpus
=
1
}
withName
:
'Generate_trait_pair'
{
container
=
'
docker://quay.io/biocontainers/jass_preprocessing_2.0.1--py_0
'
container
=
'
jass_preprocessing_2.0--py_0.sif
'
cpus
=
1
}
withName
:
'Correlation_LDSC_data'
{
container
=
"
docker://quay.io/biocontainers/
ldsc_1.0.1--py_0.sif"
container
=
"ldsc_1.0.1--py_0.sif"
cpus
=
1
}
withName
:
'Correlation_matrices'
{
container
=
'
docker://quay.io/biocontainers/jass_preprocessing_2.0.1--py_0
'
container
=
'
jass_preprocessing_2.0--py_0.sif
'
cpus
=
1
}
withName
:
'Create_inittable_LDSC'
{
container
=
'
docker://quay.io/biocontainers/jass_2.0--pyh5ca1d4c_0
'
container
=
'
jass_2.0--pyh5ca1d4c_0.sif
'
cpus
=
1
}
withName
:
'Create_inittable'
{
container
=
'
docker://quay.io/biocontainers/jass_2.0--pyh5ca1d4c_0
'
container
=
'
jass_2.0--pyh5ca1d4c_0.sif
'
cpus
=
1
}
...
...
@@ -88,7 +89,7 @@ process{
}
withName
:
'Create_project_data'
{
container
=
'
docker://quay.io/biocontainers/jass_2.0--pyh5ca1d4c_0
'
container
=
'
jass_2.0--pyh5ca1d4c_0.sif
'
cpus
=
1
}
...
...
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