local example pipeline

jass_pipeline.nf

 
 params.compute_project=true
 params.compute_LDSC_matrix=true
-params.compute_imputation=true
+params.compute_imputation=false
 
-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

@@ -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

@@ -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
     }