use the compression handling auto-opener for our eland files

[htsworkflow.git] / scripts / runfolder

diff --git a/scripts/runfolder b/scripts/runfolder
index 8b4444a2c7808d8a0a5dbff7eddca6376acf41be..bf5c5d884d2c931a6b96040a477b6bc0577ab30f 100644 (file)
--- a/scripts/runfolder
+++ b/scripts/runfolder
@@ -27,12 +27,14 @@ runfolder.py can also spit out a simple summary report (-s option)
 that contains the per lane post filter cluster numbers and the mapped 
 read counts. (The report isn't currently very pretty)
 """
+from glob import glob
 import logging
 import optparse
+import os
 import sys
 
-from htsworkflow.pipeline import runfolder
-from htsworkflow.pipeline.runfolder import ElementTree
+from htsworkflow.pipelines import runfolder
+from htsworkflow.pipelines.runfolder import ElementTree
         
 def make_parser():
     usage = 'usage: %prog [options] runfolder_root_dir'
@@ -49,9 +51,13 @@ def make_parser():
     parser.add_option('--extract-results', action='store_true',
            default=False,
            help='extract result files out of runfolder into a simpler archive')
+    parser.add_option('-o', '--output-dir', default=None,
+           help="specify the default output directory for extract results")
+
     parser.add_option('--run-xml', dest='run_xml',
            default=None,
            help='specify a run_<FlowCell>.xml file for summary reports')
+    
 
     return parser
 
@@ -64,12 +70,17 @@ def main(cmdlist=None):
         root_log = logging.getLogger()
         root_log.setLevel(logging.INFO)
 
+    logging.info('Starting htsworkflow illumina runfolder processing tool.')
     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:
-        runs.extend(runfolder.get_runs(run_dir))
+    for run_pattern in args:
+        # expand args on our own if needed
+        for run_dir in glob(run_pattern):
+            runs.extend(runfolder.get_runs(run_dir))
 
     if len(runs) > 0:
         if opt.summary:
@@ -77,7 +88,7 @@ def main(cmdlist=None):
         if opt.archive:
             runfolder.extract_run_parameters(runs)
         if opt.extract_results:
-            runfolder.extract_results(runs)
+            runfolder.extract_results(runs, opt.output_dir)
 
     return 0