readme and channel for script

README.md

+# 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)

jass_pipeline.nf

 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
 
     """
 }

nextflow.config

@@ -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

@@ -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