Commit d570bb65 authored by khalid's avatar khalid
Browse files

deal with results dir containing minus hyphen

parent d6456965
......@@ -603,7 +603,7 @@ 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 | 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'
......
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