Commit c1234ab7 authored by Hanna  JULIENNE's avatar Hanna JULIENNE

readme and channel for script

parent d2bb4089
# 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:
![workflow image](./doc/workflow.png)
params.compute_project=false
params.compute_LDSC_matrix=false
params.compute_imputation=true
params.compute_LDSC_matrix=true
params.compute_imputation=false
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
"""
}
......
......@@ -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' {
......
......@@ -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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