insert code to do ~ home directory expansion

diff --git a/scripts/runfolder b/scripts/runfolder
index bf0bcc45dcc33a02af341fe640cf76e7c6e6333b..0abbfe1c5128d1693c3443cebf8338d3023f9114 100644 (file)
--- a/scripts/runfolder
+++ b/scripts/runfolder
@@ -29,6 +29,7 @@ read counts. (The report isn't currently very pretty)
 """
 import logging
 import optparse
+import os
 import sys
 
 from htsworkflow.pipelines import runfolder
@@ -66,6 +67,8 @@ def main(cmdlist=None):
 
     runs = []
     if opt.run_xml:
+        # handle ~ shortcut
+        opt.run_xml = os.path.expanduser(opt.run_xml)
         tree = ElementTree.parse(opt.run_xml).getroot()
         runs.append(runfolder.PipelineRun(xml=tree))
     for run_dir in args: