You could also write a script in PowerShell or write an app in C#/VB. Here is an example done in PowerShell. Here is an example done in C#. Using either of these approaches, you could programmatically render the reports as you see fit. You can also create subscriptions this way as well.
PowerShell solution to the OP:
# Create a proxy to the SSRS server and give it the namespace of 'RS' to use for
# instantiating objects later. This class will also be used to create a report
# object.
$reportServerURI = "http://<SERVER>/ReportServer/ReportExecution2005.asmx?WSDL"
$RS = New-WebServiceProxy -Class 'RS' -NameSpace 'RS' -Uri $reportServerURI -UseDefaultCredential
$RS.Url = $reportServerURI
# Set up some variables to hold referenced results from Render
$deviceInfo = "<DeviceInfo><NoHeader>True</NoHeader></DeviceInfo>"
$extension = ""
$mimeType = ""
$encoding = ""
$warnings = $null
$streamIDs = $null
# Next we need to load the report. Since Powershell cannot pass a null string
# (it instead just passes ""), we have to use GetMethod / Invoke to call the
# function that returns the report object. This will load the report in the
# report server object, as well as create a report object that can be used to
# discover information about the report. It's not used in this code, but it can
# be used to discover information about what parameters are needed to execute
# the report.
$reportPath = "/PathTo/Report"
$Report = $RS.GetType().GetMethod("LoadReport").Invoke($RS, @($reportPath, $null))
# Report parameters are handled by creating an array of ParameterValue objects.
# $excelInput: either pass in as a parameter and run 50 times, or reset
# this value and run it each time with the updated excel file
$excelInput = "<ExcelFile>";
$parameters = @()
$parameters += New-Object RS.ParameterValue
$parameters[0].Name = "Excel Input File"
$parameters[0].Value = $excelInput
# Add the parameter array to the service. Note that this returns some
# information about the report that is about to be executed.
$RS.SetExecutionParameters($parameters, "en-us") > $null
# Render the report to a byte array. The first argument is the report format.
# The formats I've tested are: PDF, XML, CSV, WORD (.doc), EXCEL (.xls),
# IMAGE (.tif), MHTML (.mhtml).
$RenderOutput = $RS.Render('PDF',
$deviceInfo,
[ref] $extension,
[ref] $mimeType,
[ref] $encoding,
[ref] $warnings,
[ref] $streamIDs
)
# Convert array bytes to file and write
$OutputFile = $excelInput + ".pdf"
$Stream = New-Object System.IO.FileStream($OutputFile), Create, Write
$Stream.Write($RenderOutput, 0, $RenderOutput.Length)
$Stream.Close()