Update versions to run correctly

workflow/main.nf

@@ -189,7 +189,7 @@ process cellranger_mkfastq {
     val "${bcl.simpleName}" into bclNameCell
     file("**/outs/**/*.fastq.gz") into cellrangerCount mode flatten
     file("**/outs/fastq_path/Stats/*") into bqcPathsCell
-    file("version_ranger.txt") into version_cellranger
+    file("version_Cellranger.txt") into version_cellranger
     file("version_bcl2fastq.txt") into version_bcl2fastqCell
 
   when:
@@ -204,7 +204,7 @@ process cellranger_mkfastq {
     mkdir fq
     mkdir "fq/${bcl.simpleName}"
     find . -name "*.fastq.gz" -exec cp {} fq/${bcl.simpleName}/ \\;
-    bash versions_cellranger.sh > version_ranger.txt
+    bash versions_cellranger.sh > version_Cellranger.txt
     bash versions_bcl2fastq.sh > version_bcl2fastq.txt
     """
 }
@@ -227,7 +227,7 @@ process spaceranger_mkfastq {
     val "${bcl.simpleName}" into bclNameSpace
     file("**/outs/**/*.fastq.gz") into spacerangerCount mode flatten
     file("**/outs/fastq_path/Stats/*") into bqcPathsSpace
-    file("version_ranger.txt") into version_spaceranger
+    file("version_Spaceranger.txt") into version_spaceranger
     file("version_bcl2fastq.txt") into version_bcl2fastqSpace
 
   when:
@@ -242,7 +242,7 @@ process spaceranger_mkfastq {
     mkdir fq
     mkdir "fq/${bcl.simpleName}"
     find . -name "*.fastq.gz" -exec cp {} fq/${bcl.simpleName}/ \\;
-    bash versions_spaceranger.sh > version_ranger.txt
+    bash versions_spaceranger.sh > version_Spaceranger.txt
     bash versions_bcl2fastq.sh > version_bcl2fastq.txt
     """
 }

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>'
 

workflow/scripts/versions_cellranger.sh

@@ -6,4 +6,4 @@
 #* --------------------------------------------------------------------------
 #*
 
-cellranger mkfastq --version | grep 'cellranger mkfastq ' | sed 's/.*(\(.*\))/\1/'
\ No newline at end of file
+cellranger mkfastq --version | grep 'cellranger mkfastq ' | sed 's/.*-\(.*\))/\1/'