Set to used output dir after dryrun output for the entire WF befor insert in report

main.R

@@ -603,9 +603,9 @@ generate_pages_server <- function() {
 
     ## DRY RUN
     res <- res + '\t\t\t\tcommand = paste0("Command line to run the entire workflow:<br/>","snakemake -s /workflow/Snakefile --configfile ", paste0(input$results_dir,"/params.yml") ,\t" -d ", input$results_dir ,\t" --cores ", input$cores, " all<br/>This snakemake command needs the Snakefile and the params file of the workflow <br/><br/>What will be done :<br/>")\n'
-    res <- res + '\t\t\t\tsystem(paste0("cp ",input$results_dir,"/params.yml /tmp/dummyparams.yml &&  sed -i \'s/results_dir: [A-Za-z0-9_\\/]*/results_dir: NewResultsDir /\' /tmp/dummyparams.yml"))\n'
+    res <- res + '\t\t\t\tsystem(paste0("cp ",input$results_dir,"/params.yml /tmp/dummyparams.yml &&  sed -i \'s|results_dir: [A-Za-z0-9_/]*|results_dir: NewResultsDir |\' /tmp/dummyparams.yml"))\n'
     #run snakemeke on the dummyparams to see all the steps in final report even if the actual dir had all results !
-    res <- res + '\t\t\t\tsystem(paste0("snakemake -s /workflow/Snakefile --configfile /tmp/dummyparams.yml  -d NewResultsDir --cores ", input$cores, " all -n -p > ", input$results_dir, "/Run_Summary_mqc.html"),wait = T)\n'
+    res <- res + '\t\t\t\tsystem(paste0("snakemake -s /workflow/Snakefile --configfile /tmp/dummyparams.yml  -d NewResultsDir --cores ", input$cores, " all -n -p | sed \'s|NewResultsDir/|",input$results_dir,"|g \' > ", input$results_dir, "/Run_Summary_mqc.html"),wait = T)\n'
     res <- res + '\t\t\t\tsystem(paste0("sed -i \'1 i\\\\<pre>",command,"\' ",input$results_dir,"/Run_Summary_mqc.html"))\n'
 
   res <- res + '\t\t\tsystem2("python3",paste0("-u -m snakemake -s /workflow/Snakefile --configfile ", paste0(input$results_dir,"/params.yml") ,\t" -d ", input$results_dir ,\t" --cores ", input$cores, " all ", force, " ",rerun),wait = FALSE, stdout = paste0(input$results_dir,"/logs/runlog.txt"), stderr = paste0(input$results_dir,"/logs/runlog.txt"))\n'