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JASS_suite_pipeline
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Hervé MENAGER
JASS_suite_pipeline
Commits
c1234ab7
Commit
c1234ab7
authored
Nov 25, 2019
by
Hanna JULIENNE
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readme and channel for script
parent
d2bb4089
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14 deletions
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README.md
README.md
+9
-0
doc/workflow.png
doc/workflow.png
+0
-0
jass_pipeline.nf
jass_pipeline.nf
+15
-7
nextflow.config
nextflow.config
+4
-6
sbatch_nextflow.sh
sbatch_nextflow.sh
+1
-1
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README.md
0 → 100644
View file @
c1234ab7
# JASS analysis pipeline
We present here a nextflow pipeline to harmonize, impute and analyze jointly GWAS summary statistics.
The current pipeline integrate the following workflow:

doc/workflow.png
0 → 100644
View file @
c1234ab7
103 KB
jass_pipeline.nf
View file @
c1234ab7
params.compute_project=false
params.compute_LDSC_matrix=
fals
e
params.compute_imputation=
tru
e
params.compute_LDSC_matrix=
tru
e
params.compute_imputation=
fals
e
params.group = "$baseDir/input_files/group.txt"
group = file(params.group)
...
...
@@ -25,6 +25,8 @@ ld_channel=Channel.fromPath("/pasteur/projets/policy01/PCMA/WKD_Hanna/impute_for
Region_channel = Channel.fromPath('/pasteur/projets/policy01/PCMA/jass_analysis_pipeline/input_files/fourier_ls-all.bed')
Region_channel2 = Channel.fromPath('/pasteur/projets/policy01/PCMA/jass_analysis_pipeline/input_files/fourier_ls-all.bed')
extract_sample_size_script_channel = Channel.fromPath('/pasteur/projets/policy01/PCMA/jass_analysis_pipeline/extract_sample_size.py')
process Compute_MAF{
input:
file ref_panel from ref_chr_channel3.collect()
...
...
@@ -157,12 +159,18 @@ process Do_not_Impute_GWAS {
input:
file gwas_files from cleaned_gwas_chr_channel2.collect()
output:
file "*.txt" into not_imputed_gwas_channel
file "*.txt" into not_imputed_gwas_channel2
file "
clean_gwas/
*.txt" into not_imputed_gwas_channel
file "
clean_gwas/
*.txt" into not_imputed_gwas_channel2
when:
!params.compute_imputation
script:
"""
if [ ! -d "clean_gwas" ]
then
mkdir clean_gwas
fi
cp -L *.txt ./clean_gwas
"""
}
...
...
@@ -175,14 +183,14 @@ process Munge_LDSC_data {
input:
file clean_gwas from cleaned_gwas
file extract_sample_size_script from extract_sample_size_script_channel
output:
file "ldsc_data/*.sumstats.gz" into ldsc_data_channel
file "ldsc_data/*.sumstats.gz" into ldsc_data_channel_bis
when:
params.compute_LDSC_matrix
"""
Nsamp=\$(python2.7 ${baseDir}/extract_sample_size.py ${clean_gwas} ${GWAS_labels})
Nsamp=\$(python2.7 ${extract_sample_size_script} ${clean_gwas} ${GWAS_labels})
if [ ! -d "ldsc_data" ]
then
...
...
@@ -301,7 +309,7 @@ process Create_inittable {
date_init=\$(date +"%m_%d_%Y-%H:%M")
init_name="inittable_NO_LDSC_\$date_init.hdf5"
jass create-inittable --input-data-path "\$e" --regions-map-path ${Regions} --description-file-path ${GWAS_labels} --init-table-path inittable_no_LDSC.hdf5
jass create-inittable --input-data-path "\$e" --regions-map-path ${Regions} --description-file-path ${GWAS_labels} --init-table-path inittable_no_LDSC.hdf5
--init-covariance-path ${baseDir}/Correlation_matrices/Covariance_matrix_H0.csv
"""
}
...
...
nextflow.config
View file @
c1234ab7
...
...
@@ -21,12 +21,12 @@ singularity {
process
{
executor
=
'slurm'
maxErrors
=
10
maxRetries
=
3
maxErrors
=
10
maxRetries
=
3
maxForks
=
400
queueSize
=
500
errorStrategy
=
'retry'
cache
=
'deep'
cache
=
'deep'
withName
:
'Compute_MAF'
{
...
...
@@ -44,7 +44,6 @@ process{
cpus
=
1
}
withName
:
'Clean_GWAS'
{
//
container
=
'jass_preprocessing_1.0--py_0.sif'
cpus
=
1
...
...
@@ -55,7 +54,6 @@ process{
cpus
=
1
}
withName
:
'Munge_LDSC_data'
{
container
=
'ldsc_1.0.1--py_0.sif'
cpus
=
1
...
...
@@ -63,7 +61,7 @@ process{
withName
:
'Generate_trait_pair'
{
container
=
'jass_preprocessing_1.0--py_0.sif'
cpus
=
1
cpus
=
1
}
withName
:
'Correlation_LDSC_data'
{
...
...
sbatch_nextflow.sh
View file @
c1234ab7
...
...
@@ -33,7 +33,7 @@ module load singularity/3.4.0
cd
/pasteur/projets/policy01/PCMA/jass_analysis_pipeline
source
/pasteur/homes/hjulienn/jass_suite/jass_suite/bin/activate
nextflow run jass_pipeline.nf
-with-report
jass_report.html
-with-timeline
jass_timeline.html
-with-dag
dag.png
nextflow run jass_pipeline.nf
-
resume
-
with-report
jass_report.html
-with-timeline
jass_timeline.html
-with-dag
dag.png
# Finish the script
deactivate
exit
0
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