Q:

RShiny : checkBox format

Current status of the boxes : 

I am unable to improve the following things :

Have the text in a row by itself(The Select the modules... one)
The box and text are not aligned on the same line.
The checkboxes on the top line are slightly truncated.(the remaining is encircled below)
The labels(a to j) need to be in white bold text.

This is what I have tried so far :
ui.R :
library(shiny)
controls <- list(tags$div(align = 'left', 
                class = 'multicol', 
                checkboxGroupInput(inputId  = 'modules', 
                                   label    = "Step 1 : Select the modules to be executed", 
                                   choices  = c(process_names),
                                   selected = "",
                                   inline   = FALSE)))
shinyUI(fluidPage(
  tags$style(type='text/css', "label {font-size: 22px; }            # controls the text of check-boxes
             .form-group {margin-top: 5px; margin-bottom: 5px;}
             .nav-tabs {font-family:'arial';font-size:20px}
             #sidebar {background-color: #5C97BF;}
             #mainbar {background-color: #5C97BF;}
             body { background-color: #002B55;}
             input[type=checkbox] {transform: scale(2);}
             .multicol {height: 200px; -webkit-column-count: 4; 
             -moz-column-count: 4;    /* Firefox */
             column-count: 4; -moz-column-fill: auto;-column-fill: auto;} # increases the size of checkboxes
             div.checkbox {margin-top: 10px;color:'#FFFFFF';font-weight: bold; }
             .btn {display:block;height: 60px;width: 40px;border-radius: 50%;} # for actionButton
             "),

  sidebarLayout(
    position = "left",
    sidebarPanel(controls),
    mainPanel()
  )
))

server.R
shinyServer(
  function(input, output){

  }
)

A:

Here's fixed code for your app:
library(shiny)
process_names <- letters[1:13]
controls <- tags$div(
  tags$label("Step 1 : Select the modules to be executed"),
  tags$div(align = 'left', 
           class = 'multicol', 
           checkboxGroupInput(inputId  = 'modules', 
                              label    = NULL, 
                              choices  = c(process_names),
                              selected = "",
                              inline   = FALSE)))
ui<-(fluidPage(
  tags$style(type='text/css', "label {font-size: 22px; }           
             .form-group {margin-top: 5px; margin-bottom: 5px;}
             .nav-tabs {font-family:'arial';font-size:20px}
             #sidebar {background-color: #5C97BF;}
             #mainbar {background-color: #5C97BF;}
             body { background-color: #002B55;}
             input[type=checkbox] {transform: scale(2);margin-top:10px;}
             .multicol {height: 200px; -webkit-column-count: 4; 
             -moz-column-count: 4;    /* Firefox */
             column-count: 4; -moz-column-fill: auto;-column-fill: auto;} 
             .checkbox {margin-top:-5px;}
             .btn {display:block;height: 60px;width: 40px;border-radius: 50%;} 
             #modules .checkbox label span {font-weight:bold;}
             label {color:#fff;}
             "),

  sidebarLayout(
    position = "left",
    sidebarPanel(controls),
    mainPanel()
  )
  ))

server<-function(input,output){}

shinyApp(ui,server)

This takes care of all your issues. Note that one big problem you had (that took me a long time to debug!) is that you cannot use # as comments inside CSS. That breaks your CSS. You can only use /* comment here */ as comments in CSS.

