pipeline maintenance and update

README.md

@@ -46,4 +46,8 @@ The following Item are necessary to run JASS pipeline on real data
 
 * --output_folder : A path toward a folder to write pipeline results (inittable, worktable...). by default results will be publish in the workflow directory.
 
-Parameters can be specified in command line or by editing the
+##  Usage Example on HPC Cluster
+
+If you are working with a HPC server (Slurm job scheduler), you can adapt the nextflow_sbatch.config file and launch the pipeline with a command like:
+
+sbatch --mem-per-cpu 32G -p common,dedicated,ggs --qos=long --wrap "module load java/13.0.2;module load singularity/3.8.3;module load graphviz/2.42.3;./nextflow run imputation_only.nf  -with-report imput_report.html -with-timeline imput_timeline.html -c nextflow_sbatch.config -qs 300"

correlation.nf

+params.output_folder = "${baseDir}"
+
+/* Script channels*/
+extract_sample_size_script_channel = Channel.fromPath("${baseDir}/extract_sample_size.py")
+generate_trait_pairs_channel = Channel.fromPath("${baseDir}/generate_trait_pairs.py")
+parse_correlation_channel = Channel.fromPath("${baseDir}/parse_correlation_results.py")
+
+ldsc_data_channel = Channel.fromPath("${baseDir}/ldsc_data/data_*.sumstats.gz")
+ldsc_data_channel_bis = Channel.fromPath("${baseDir}/ldsc_data/data_*.sumstats.gz")
+/*
+    process related to LD-score calculation
+*/
+
+
+process Generate_trait_pair {
+    time '1h'
+    queue 'dedicated,common,ggs'
+    input:
+        file generate_trait_pairs_script from generate_trait_pairs_channel
+        file ldsc_data from ldsc_data_channel.unique().collect()
+    output:
+        file "pairs_chunk_*.txt" into combi_channel mode flatten
+
+    """
+    python3 ${generate_trait_pairs_script}
+    """
+}
+
+process Correlation_LDSC_data {
+    memory {8.GB * task.attempt}
+    time {24.h * task.attempt}
+    queue 'dedicated,common,ggs'
+    publishDir "${params.output_folder}/cor_data/", pattern: "*.log", mode: 'copy'
+    input:
+        file trait_pair from combi_channel
+        file ldsc_data from ldsc_data_channel_bis.unique().collect()
+    output:
+        file "*.log" into cor_log_channel
+
+    """
+    export OMP_NUM_THREADS=1
+    echo ${trait_pair}
+    IFS=';' read -ra my_trait <<< "\$(cat ${trait_pair})"
+    i=1
+
+    for trait_p in \${my_trait[@]}
+    do
+
+        echo \$trait_p
+        trait1=\$(echo \$trait_p | cut -d '.' -f1 | cut -d '_' -f2,3)
+        trait2=\$(echo \$trait_p | cut -d ',' -f2 | cut -d '.' -f1 | cut -d '_' -f2,3)
+
+        ldsc.py --rg \$trait_p --out \${trait1}-_-\${trait2} --ref-ld-chr ${baseDir}/eur_w_ld_chr/ --w-ld-chr ${baseDir}/eur_w_ld_chr/
+
+    done
+    """
+}
+
+
+process Correlation_matrices {
+
+    publishDir "${params.output_folder}/Correlation_matrices/", pattern: "*.csv", mode: 'copy'
+    time '1h'
+    queue 'dedicated,common,ggs'
+    input:
+        file parsing_script from parse_correlation_channel
+        file ldsc_data from cor_log_channel.collect()
+
+    """
+    python3 ${parsing_script}
+
+    """
+}

imputation_only.nf

+params.ref_panel = '/pasteur/zeus/projets/p02/GGS_JASS/1._DATA/ImpG_refpanel/'
+
+params.region = "${baseDir}/input_files/fourier_ls-all.bed"
+params.output_folder = "${baseDir}"
+
+Region_channel = Channel.fromPath(params.region)
+chr_channel = Channel.from(1..22)
+
+ref_chr_channel=Channel.fromPath(params.ref_panel+"/chr*.eur.1pct.bim")
+ld_channel=Channel.fromPath("/pasteur/zeus/projets/p02/GGS_JASS/WKD_Hanna/impute_for_jass/ld_block_new_plink/*.ld")
+
+harmonized_GWAS_files=Channel.fromPath("/pasteur/zeus/projets/p02/GGS_JASS/jass_analysis_pipeline/harmonized_GWAS_files/*.txt")
+
+process Impute_GWAS {
+    publishDir "${params.output_folder}", pattern: "imputed_GWAS/*.txt", mode: 'copy'
+    memory {8.GB * task.attempt}
+    time {24.h * task.attempt}
+    maxRetries = 4
+    queue 'dedicated,ggs,common'
+    input:
+        file gwas_files from harmonized_GWAS_files
+        file ref_file from ref_chr_channel.collect()
+        file ld_file from ld_channel.collect()
+    output:
+        file "imputed_GWAS/*.txt" into imputed_gwas_channel
+        file "imputed_GWAS/*.txt" into imputed_gwas_channel2
+    script:
+    """
+    mkdir -p imputed_GWAS
+
+    chrom=\$(echo ${gwas_files} | cut -d '_' -f4 | cut -d "." -f1)
+    study=\$(echo ${gwas_files} | cut -d '_' -f2,3)
+
+    echo \$chrom
+    echo \$study
+
+    raiss --chrom \${chrom} --gwas \${study} --ref-folder ./ --R2-threshold 0.6 --eigen-threshold 1.0 --ld-folder ./ --zscore-folder ./ --output-folder ./imputed_GWAS --ref-panel-suffix .eur.1pct.bim
+    """
+}

nextflow.config

-dag {
-    enabled = true
-    file = 'dag.dot'
-}
-
-report {
-       enabled = true
-       file = 'nextflow_logs/report.html'
-}
-
-trace {
-        enabled = true
-        file = 'nextflow_logs/trace.txt'
-}
-
-singularity {
-            enabled = true
-            autoMounts = true
-            runOptions = '--home $HOME:/home/$USER'
-}
-
-process{
-        executor='local'
-        maxErrors=10
-        maxRetries=3
-        maxForks=400
-        queueSize=500
-        errorStrategy='finish'
-        cache='deep'
-
-
-  withName: 'Compute_MAF' {
-    container='docker://quay.io/biocontainers/plink:1.90b5--heea4ae3_1'
-    cpus=1
-    }
-
-    withName: 'create_WG_reference_panel' {
-		container='docker://quay.io/biocontainers/jass_preprocessing:2.0.1--py_0'
-		cpus=1
-	}
-
-    withName: 'meta_data_GWAS' {
-        cpus=1
-    }
-
-    withName: 'Clean_GWAS' {
-        
-        cpus=1
-    }
-
-    withName: 'Impute_GWAS' {
-        container='docker://quay.io/biocontainers/raiss:3.1--pyhdfd78af_0'
-        cpus=1
-    }
-
-    withName: 'Munge_LDSC_data' {
-
-      container='docker://quay.io/biocontainers/ldsc:1.0.1--py_0'
-        cpus=1
-    }
-
-    withName: 'Generate_trait_pair' {
-    container='docker://quay.io/biocontainers/jass_preprocessing:2.0.1--py_0'
-    cpus=1
-    }
-
-    withName: 'Correlation_LDSC_data' {
-      container="docker://quay.io/biocontainers/ldsc:1.0.1--py_0"
-        cpus=1
-    }
-
-    withName: 'Correlation_matrices' {
-      container='docker://quay.io/biocontainers/jass_preprocessing:2.0.1--py_0'
-        cpus=1
-    }
-
-    withName: 'Create_inittable_LDSC' {
-      container='docker://quay.io/biocontainers/jass:2.0--pyh5ca1d4c_0'
-        cpus=1
-    }
-
-    withName: 'Create_inittable' {
-      container='docker://quay.io/biocontainers/jass:2.0--pyh5ca1d4c_0'
-        cpus=1
-    }
-
-    withName: 'get_pheno_group' {
-        cpus=1
-    }
-
-    withName: 'Create_project_data' {
-        container='docker://quay.io/biocontainers/jass:2.0--pyh5ca1d4c_0'
-        cpus=1
-    }
-
-}

nextflow_slurm.config → nextflow_sbatch.config

@@ -16,27 +16,28 @@ trace {
 singularity {
             enabled = true
             autoMounts = true
-            runOptions = '--home $HOME:/home/$USER'
+            runOptions = '--home $HOME:/home/$USER -B /pasteur/zeus/projets/p02/GGS_JASS/jass_analysis_pipeline/'
+}
+executor {
+    submitRateLimit = '10 sec'
 }
-
 process{
-        executor='local'
-        maxErrors=10
-        maxRetries=3
+        executor='slurm'
+        maxErrors=20
+        maxRetries=4
         maxForks=400
-        queueSize=500
-        errorStrategy='finish'
+        queueSize = 500
+        errorStrategy='retry'
         cache='deep'
 
 
-    withName: 'Compute_MAF' {
-        container='plink_1.90b5--heea4ae3_0.sif'
-        cpus=1
-        }
-
+  withName: 'Compute_MAF' {
+      container='plink_1.90b5--heea4ae3_0.sif'
+      cpus=1
+      }
 
     withName: 'create_WG_reference_panel' {
-		container='jass_preprocessing_2.0--py_0.sif'
+		container='jass_preprocessing_2.1--pyhdfd78af_0.sif'
 		cpus=1
 	}
 
@@ -45,12 +46,13 @@ process{
     }
 
     withName: 'Clean_GWAS' {
-//      container='jass_preprocessing_2.0--py_0.sif'
-        cpus=1
+      memory = '16G'
+      cpus=1
     }
 
     withName: 'Impute_GWAS' {
-      container="raiss_2.0--py_0.sif"
+        memory = '8G'
+        container='raiss_3.1--pyhdfd78af_0.sif'
         cpus=1
     }
 
@@ -60,7 +62,7 @@ process{
     }
 
     withName: 'Generate_trait_pair' {
-    container='jass_preprocessing_2.0--py_0.sif'
+    container='jass_preprocessing_2.1--pyhdfd78af_0.sif'
     cpus=1
     }
 
@@ -70,17 +72,17 @@ process{
     }
 
     withName: 'Correlation_matrices' {
-      container='jass_preprocessing_2.0--py_0.sif'
+      container='jass_preprocessing_2.1--pyhdfd78af_0.sif'
         cpus=1
     }
 
     withName: 'Create_inittable_LDSC' {
-      container='jass_2.0--pyh5ca1d4c_0.sif'
+      container='jass_2.2--pyhb7b1952_0.sif'
         cpus=1
     }
 
     withName: 'Create_inittable' {
-      container='jass_2.0--pyh5ca1d4c_0.sif'
+      container='jass_2.2--pyhb7b1952_0.sif'
         cpus=1
     }
 
@@ -89,7 +91,7 @@ process{
     }
 
     withName: 'Create_project_data' {
-      container='jass_2.0--pyh5ca1d4c_0.sif'
+      container='jass_2.2--pyhb7b1952_0.sif'
         cpus=1
     }