Buzz lightyear

Add Spaceranger to the mkfastq pipeline

workflow/scripts/generate_versions.py

@@ -25,12 +25,12 @@ logger.addHandler(logging.NullHandler())
 logger.propagate = False
 logger.setLevel(logging.INFO)
 
+
 SOFTWARE_REGEX = {
     'Pipeline': ['version_pipeline.txt', r"(\S+)"],
     'Nextflow': ['version_nextflow.txt', r"(\S+)"],
     'python': ['version_python.txt', r"(\S+)"],
     #'pigz': ['version_pigz.txt', r"(\S+)"],
-    '10x-ranger': ['version_ranger.txt', r"(\S+)"],
     'bcl2fastq': ['version_bcl2fastq.txt', r"(\S+)"],
     'fastqc': ['version_fastqc.txt', r"(\S+)"],
 }
@@ -56,6 +56,18 @@ def get_args():
     return args
 
 
+def rangerType(files):
+    '''Determine Type of Ranger being used'''
+
+    for fname in files:
+            ranger = re.findall("version_(.*)ranger.txt", fname)
+            if not ranger: continue
+            ranger_type = ranger[0]+"ranger"
+            SOFTWARE_REGEX[ranger_type] = [fname, r"(\S+)"]
+
+    return ranger_type
+
+
 def check_files(files):
     '''Check if version files are found.'''
 
@@ -77,12 +89,14 @@ def main():
 
     out_filename = output + '_mqc.yaml'
 
+    ranger_type = rangerType(files)
+
     results = OrderedDict()
     results['Pipeline'] = '<span style="color:#999999;\">N/A</span>'
     results['Nextflow'] = '<span style="color:#999999;\">N/A</span>'
     results['python'] = '<span style="color:#999999;\">N/A</span>'
     #results['pigz'] = '<span style="color:#999999;\">N/A</span>'
-    results['10x-ranger'] = '<span style="color:#999999;\">N/A</span>'
+    results[ranger_type] = '<span style="color:#999999;\">N/A</span>'
     results['bcl2fastq'] = '<span style="color:#999999;\">N/A</span>'
     results['fastqc'] = '<span style="color:#999999;\">N/A</span>'
 
@@ -95,7+109,7 @@
             versions = x.read()
             match = re.search(v[1], versions)
             if match:
                 results[k] = "v{}".format(match.group(1))
 
     # Dump to YAML
     print(