From ae2bf51394e5a028b895181523df68123cbf5f68 Mon Sep 17 00:00:00 2001 From: gmillot <gael.millot@pasteur.fr> Date: Mon, 27 Jun 2022 17:35:41 +0200 Subject: [PATCH] release v3.1: version used for dyslexia analysis --- README.md | 5 +++++ bin/miami.R | 4 ++-- vcf_fisher.config | 8 ++++---- 3 files changed, 11 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index debb259..44c9ebb 100644 --- a/README.md +++ b/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 diff --git a/bin/miami.R b/bin/miami.R index 4548bfa..e9b4440 100644 --- a/bin/miami.R +++ b/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( diff --git a/vcf_fisher.config b/vcf_fisher.config index 00ab124..249cb5d 100644 --- a/vcf_fisher.config +++ b/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' -- GitLab