release v3.1: version used for dyslexia analysis

README.md

@@ -203,6 +203,11 @@ Gitlab developers
 <br /><br />
 ## WHAT'S NEW IN
 
+### v3.1
+
+1) version used for dyslexia analysis
+
+
 ### v3.0
 
 1) vcf_ficher.nf now parallelized for all the genome

bin/miami.R

@@ -406,14 +406,14 @@ if(length(obs) > 0 & nrow(obs) > 0){
         y = 0, 
         yend = -0.05, 
         size = 1
-        ))
+    ))
 
 
     fin.plot1 <- suppressMessages(suppressWarnings(eval(parse(text = paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + ")))))
 
     tempo.gg.name2 <- "gg.indiv.plot."
     tempo.gg.count2 <- 0
-    assign(paste0(tempo.gg.name2, tempo.gg.count2 <- tempo.gg.count2 + 1), ggplot(obs, aes_string(x = "coord", y = "neg.log10.p")))
+    assign(paste0(tempo.gg.name2, tempo.gg.count2 <- tempo.gg.count2 + 1), ggplot(obs, aes_string(x = "coord", y = "OR")))
     assign(paste0(tempo.gg.name2, tempo.gg.count2 <- tempo.gg.count2 + 1), geom_point(aes(color=as.factor(chr)), alpha=0.5, size=1))
     assign(paste0(tempo.gg.name2, tempo.gg.count2 <- tempo.gg.count2 + 1), scale_color_manual(values = rep(c("grey", "skyblue"), 25)))
     assign(paste0(tempo.gg.name2, tempo.gg.count2 <- tempo.gg.count2 + 1), scale_x_continuous(

vcf_fisher.config

@@ -16,13 +16,13 @@
 
 // variables exported to the main.nf environment. See https://www.nextflow.io/docs/latest/config.html#scope-env
 env {
-    sample_path = "/pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/dataset/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz" // vcf. Example: /pasteur/zeus/projets/p02/ghfc_wgs_zeus/WGS/Dyslexia/vcf/Dyslexia.gatk-vqsr.splitted.norm.vep.merged.vcf.gz
+    sample_path = "/pasteur/zeus/projets/p02/ghfc_wgs_zeus/WGS/Dyslexia/vcf/Dyslexia.gatk-vqsr.splitted.norm.vep.merged.vcf.gz" // "/pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/dataset/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz" // vcf. Example: /pasteur/zeus/projets/p02/ghfc_wgs_zeus/WGS/Dyslexia/vcf/Dyslexia.gatk-vqsr.splitted.norm.vep.merged.vcf.gz
     //Warning: do not write the out_path now. See below. If written here, the one below is not considered"
     ped_path = "/pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/dataset/Dyslexia.pedigree.txt" // pedigree
     chr_path = "/pasteur/zeus/projets/p01/BioIT/gmillot/reference_genomes/human hg19_grch37/hg19_grch37p5_chr_size_cumul.txt"
     region = "None" // region to parse. Write "chr7:0-147000000, chr10:1000000-2000000" for a single region, "chr7:0-147000000, chr10:1000000-2000000" if two regions, ""chr7" for a whole chromosome, "chr7, chr1" for two chromosomes and "None" for the complete genome // Warning : replace eval() by ast.literal_eval() from ast package in the main py code ?
     y_lim1 = 5 // max y-axis limit of the top panel in the miami plot, in log10, i.e., 5 means up to score 10^5
-    y_lim2 = 5 // max y-axis limit of the bottom panel in the miami plot, in log10, i.e., 5 means up to score 10^5
+    y_lim2 = 20 // max y-axis limit of the bottom panel in the miami plot, in log10, i.e., 5 means up to score 10^5
     cute_path = "https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/v11.4.0/cute_little_R_functions.R" // single character string indicating the file (and absolute pathway) of the required cute_little_R_functions toolbox. With ethernet connection available, this can also be used: "https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/raw/v5.1.0/cute_little_R_functions.R" or local "C:\\Users\\Gael\\Documents\\Git_projects\\cute_little_R_functions\\cute_little_R_functions.R"
 }
 
@@ -145,8 +145,8 @@ process {
 // directives for all the processes
     // executor='local' // no need because already defined above in the executor scope
     if(system_exec == 'slurm'){
-        queue = "$fastqueue"
-        clusterOptions = "$fastqos $add_options"
+        queue = "$longqueue"
+        clusterOptions = "$longqos $add_options"
         scratch=false
         maxRetries=30
         errorStrategy='retry'