Add checkbox to rerun incomplete

main.R

@@ -677,7 +677,8 @@ generate_pages_server <- function() {
 
   # RUN
   res <- res + '\t\tforce = force_rule(input$force_from)\n'
-  res <- res + '\t\tsystem2("python3",paste0("-u -m snakemake -s /workflow/Snakefile --configfile ", paste0(input$results_dir,"/params.yml") ,\t" -d ", input$results_dir ,\t" --cores ", input$cores, " all ", force),wait = FALSE, stdout = paste0(input$results_dir,"/logs/runlog.txt"), stderr = paste0(input$results_dir,"/logs/runlog.txt"))\n'
+  res <- res + '\t\trerun = input$rerun_incomplete ? "--rerun-incomplete" : ""\n'
+  res <- res + '\t\tsystem2("python3",paste0("-u -m snakemake -s /workflow/Snakefile --configfile ", paste0(input$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'
   res <- res + '\t\ttags$iframe(src="results/multiqc_report.html",width="100%", height="900px")},\n'
   res <- res + '\t\terror = function(e){\n'
   res <- res + '\t\t\tsystem(paste0("touch ",input$results_dir,"/logs/workflow_end.error"),wait = T)\n'
@@ -920,7 +921,7 @@ generate_app <- function() {
     res <- res + "tabReport = fluidPage(box(title = 'Report :', width = 12, status = 'primary', collapsible = TRUE, solidHeader = TRUE, uiOutput('report_html')))\n"
   }
 
-  res <- res + 'tabRUN = fluidPage(box(title = \'Run :\', width = 12 , status = \'primary\', collapsible = TRUE, solidHeader = TRUE, uiOutput(\'run_out\',style = \'overflow-y: scroll; height: 600px\')),actionButton("unlock", "Unlock the directory in case of previous failure"))\n'
+  res <- res + 'tabRUN = fluidPage(box(title = \'Run :\', width = 12 , status = \'primary\', collapsible = TRUE, solidHeader = TRUE, uiOutput(\'run_out\',style = \'overflow-y: scroll; height: 600px\')),actionButton("unlock", "Unlock the directory in case of previous failure"), checkboxInput("rerun_incomplete", "Check in case of incomplete jobs to rerun", value = FALSE, width = NULL))\n'
   
   res <- res + 'source("./R/menugauche.R", local=T)\n\n'