From 4f51a68dc7d77c3b2cf8f5a3c9bfca8a2affd86d Mon Sep 17 00:00:00 2001 From: Mia <mia.legras@etu.u-paris.fr> Date: Mon, 4 Jul 2022 11:39:46 +0200 Subject: [PATCH] derniere version --- .gitignore | 5 ++++- bin/slith_part1.R | 4 ++-- bin/slith_part2.R | 10 +++++----- nextflow.config | 9 +++++---- script.nf | 10 +++++----- 5 files changed, 21 insertions(+), 17 deletions(-) diff --git a/.gitignore b/.gitignore index 0698ded..65be237 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,7 @@ docker docs other -README.md \ No newline at end of file +README.md +.nextflow +singularity +work \ No newline at end of file diff --git a/bin/slith_part1.R b/bin/slith_part1.R index 8407ae5..ccbfb25 100755 --- a/bin/slith_part1.R +++ b/bin/slith_part1.R @@ -92,7 +92,7 @@ serp.symmet.input <- as.logical(toupper(args[39])) adj_mean <- args[40] hiccompare_graph <- args[41] intern_funct_check <- args[42] -mask_plots <- args[43] +mask_plot <- args[43] if (theo.import) { theo.mat.ch1 <- args[44] theo.mat.ch2 <- args[45] @@ -146,7 +146,7 @@ param.list <- c( "adj_mean", "hiccompare_graph", "intern_funct_check", - "mask_plots", + "mask_plot", if (theo.import) { "theo.file.name1" "theo.file.name2" diff --git a/bin/slith_part2.R b/bin/slith_part2.R index 389969b..3073cf5 100755 --- a/bin/slith_part2.R +++ b/bin/slith_part2.R @@ -35,7 +35,7 @@ serp.symmet.input <- as.logical(toupper(args[29])) adj_mean <- args[30] hiccompare_graph <- args[31] intern_funct_check <- args[32] -mask_plots <- args[33] +mask_plot <- args[33] warning.message <- NULL ini.date <- Sys.time() @@ -114,13 +114,13 @@ if (activate.pdf == TRUE) { ## end import mat1.obs.serp <- - as.matrix(read.table(obs.file1, header = FALSE)) + as.matrix(read.table(obs.file1, header = FALSE, sep = ",")) mat2.obs.serp <- - as.matrix(read.table(obs.file2, header = FALSE)) + as.matrix(read.table(obs.file2, header = FALSE, sep = ",")) mat1.theo.serp <- - as.matrix(read.table(theo.file1, header = FALSE)) + as.matrix(read.table(theo.file1, header = FALSE, sep = ",")) mat2.theo.serp <- - as.matrix(read.table(theo.file2, header = FALSE)) + as.matrix(read.table(theo.file2, header = FALSE, sep = ",")) # end export of binned obs and theo matrices ################ end serpentine diff --git a/nextflow.config b/nextflow.config index 774de47..998af4e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -20,10 +20,11 @@ env { project_name = "slitherine" //// path and files + slith_path = "/home/rsg/mia/gitlab" lib_path = "NULL" - in_path = "/home/ishimia" - out_path = "/home/ishimia/result" - matrix_file1 = "GSM2870407_mat_BC70_TACT_wt_MM_30C.txt" + in_path = "/home/rsg/mia/gitlab/matrices_Mia" + out_path = "/home/rsg/mia/gitlab/result" + matrix_file1 = "GSM2870423_mat_BC172_CGGT_wt_LB_30C_rep1.txt" matrix_file2 = "GSM2870422_mat_BC172_CGGT_wt_LB_30C.txt" serp_binning = true thr_tot = '70' @@ -74,7 +75,7 @@ env { adj_mean = "$projectDir/bin/adj_mean.R" hiccompare_graph = "$projectDir/bin/hiccompare_graph.R" intern_funct_check = "$projectDir/bin/intern_funct_check.R" - mask_plots = "$projectDir/bin/mask_plots.R" + mask_plot = "$projectDir/bin/mask_plot.R" } //////// end variables that will be used only in the script.nf diff --git a/script.nf b/script.nf index 4ff1d8f..b525656 100644 --- a/script.nf +++ b/script.nf @@ -107,7 +107,7 @@ process PRE_SERPENTINE { val adj_mean val hiccompare_graph val intern_funct_check - val mask_plots + val mask_plot if(theo_import){ file mat1_theo from theo_mat_ch1 file mat2_theo from theo_mat_ch2 @@ -133,7 +133,7 @@ process PRE_SERPENTINE { "${step_factor}" "${ratio_normalization}" "${activate_pdf}" "${optional_text}" \ "${width_wind}" "${height_wind}" "${dot_size}" "${line_size}" "${heatmap_text_size}" \ "${text_size}" "${title_text_size}" "${raster}" "${transfo}" "${warn_secu}" \ - "${serp_symmet_input}" "${adj_mean}" "${hiccompare_graph}" "${intern_funct_check}" "${mask_plots}" \ + "${serp_symmet_input}" "${adj_mean}" "${hiccompare_graph}" "${intern_funct_check}" "${mask_plot}" \ "${mat1_theo}" "${mat2_theo}" "${theo_path_in}" """ else @@ -146,7 +146,7 @@ process PRE_SERPENTINE { "${step_factor}" "${ratio_normalization}" "${activate_pdf}" "${optional_text}" \ "${width_wind}" "${height_wind}" "${dot_size}" "${line_size}" "${heatmap_text_size}" \ "${text_size}" "${title_text_size}" "${raster}" "${transfo}" "${warn_secu}" "${serp_symmet_input}" \ - "${adj_mean}" "${hiccompare_graph}" "${intern_funct_check}" "${mask_plots}" + "${adj_mean}" "${hiccompare_graph}" "${intern_funct_check}" "${mask_plot}" """ } @@ -215,7 +215,7 @@ if (serp_binning == true){ val adj_mean val hiccompare_graph val intern_funct_check - val mask_plots + val mask_plot output: path "*.txt" @@ -230,7 +230,7 @@ if (serp_binning == true){ "${step_factor}" "${ratio_normalization}" "${activate_pdf}" "${optional_text}" \ "${width_wind}" "${height_wind}" "${dot_size}" "${line_size}" "${heatmap_text_size}" \ "${text_size}" "${title_text_size}" "${raster}" "${transfo}" "${warn_secu}" \ - "${serp_symmet_input}" "${adj_mean}" "${hiccompare_graph}" "${intern_funct_check}" "${mask_plots}" + "${serp_symmet_input}" "${adj_mean}" "${hiccompare_graph}" "${intern_funct_check}" "${mask_plot}" """ } } -- GitLab