Update workflow/main.nf, workflow/scripts/check_design.py,...

Update workflow/main.nf, workflow/scripts/check_design.py, workflow/scripts/generate_references.py, workflow/scripts/generate_versions.py, workflow/scripts/filename_check.sh, workflow/tests/test_check_design.py, workflow/tests/test_count.py, workflow/tests/test_multiqc.py, workflow/tests/test_versions.py files

workflow/main.nf

 #!/usr/bin/env nextflow
-
-// Path to an input file, or a pattern for multiple inputs
-// Note - $baseDir is the location of this workflow file main.nf
+/*
+main.nf
+*
+* --------------------------------------------------------------------------
+* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/develop/LICENSE)
+* --------------------------------------------------------------------------
+*
+*/
 
 // Define Input variables
 params.name = "run"
@@ -64,6 +69,7 @@ outDir = params.outDir
 multiqcConf = params.multiqcConf
 references = params.references
 
+
 process checkDesignFile {
 
   tag "${name}"
@@ -324,7 +330,6 @@ process versions {
 metricsSummary = metricsSummary211.mix(metricsSummary301, metricsSummary302, metricsSummary310)
 
 
-// Generate MultiQC Report
 process multiqc {
 
   tag "${name}"
@@ -348,4 +353,4 @@ process multiqc {
     multiqc -c ${multiqcConf} .
     """
 
-}
+}
\ No newline at end of file

workflow/scripts/check_design.py

 #!/usr/bin/env python3
-
-'''Check if design file is correctly formatted and matches files list.'''
+#check_design.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/develop/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import argparse
 import logging
@@ -11,8 +15,6 @@ For more details:
         %(prog)s --help
 '''
 
-# SETTINGS
-
 logger = logging.getLogger(__name__)
 logger.addHandler(logging.NullHandler())
 logger.propagate = False
@@ -61,6 +63,7 @@ def check_design_headers(design):
     
     return design
 
+
 def check_files(design, fastq):
     '''Check if design file has the files found.'''
 
@@ -104,4 +107,4 @@ def main():
     new_design_df.to_csv('design.checked.csv', header=True, sep=',', index=False)
 
 if __name__ == '__main__':
-    main()
+    main()
\ No newline at end of file

workflow/scripts/filename_check.sh

 #!/bin/bash
 #filename_check.sh
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/develop/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 usage() {
   echo "-r  --ref file"
@@ -28,4 +33,4 @@ if [ $(echo "${ref}" | tr -d ' ') != "${ref}" ]; then
   echo "Error: Spaces found in Reference Files"
   echo ${ref}
   exit 21
-fi
+fi
\ No newline at end of file

workflow/scripts/generate_references.py

 #!/usr/bin/env python3
-
-'''Make header for HTML of references.'''
+#generate_references.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/develop/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import argparse
 import subprocess
@@ -12,8 +16,6 @@ For more details:
         %(prog)s --help
 '''
 
-# SETTINGS
-
 logger = logging.getLogger(__name__)
 logger.addHandler(logging.NullHandler())
 logger.propagate = False
@@ -65,4 +67,4 @@ def main():
 
 
 if __name__ == '__main__':
-    main()
+    main()
\ No newline at end of file

workflow/scripts/generate_versions.py

 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-'''Make YAML of software versions.'''
+#generate_versions.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/develop/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 from __future__ import print_function
 from collections import OrderedDict
@@ -15,7 +18,6 @@ For more details:
         %(prog)s --help
 '''
 
-# SETTINGS
 logger = logging.getLogger(__name__)
 logger.addHandler(logging.NullHandler())
 logger.propagate = False
@@ -104,4 +106,4 @@ def main():
 
 
 if __name__ == '__main__':
-    main()
+    main()
\ No newline at end of file

workflow/tests/test_check_design.py

 #!/usr/bin/env python3
+#test_check_design.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/develop/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd
@@ -22,4 +28,4 @@ def test_count302_design():
 
 @pytest.mark.count310
 def test_count310_design():
-    assert os.path.exists(os.path.join(test_output_path, 'design.checked.csv'))
+    assert os.path.exists(os.path.join(test_output_path, 'design.checked.csv'))
\ No newline at end of file

workflow/tests/test_count.py

 #!/usr/bin/env python3
+#test_count.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/develop/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd
@@ -27,4 +33,4 @@ def test_count302_count():
 @pytest.mark.count310
 def test_count310_count():
     assert os.path.exists(os.path.join(test_output_path, 'count310', 'sample1_metrics_summary.tsv'))
-    assert os.path.exists(os.path.join(test_output_path, 'count310', 'sample1', 'outs'))
+    assert os.path.exists(os.path.join(test_output_path, 'count310', 'sample1', 'outs'))
\ No newline at end of file

workflow/tests/test_multiqc.py

 #!/usr/bin/env python3
+#test_multiqc.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/develop/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd
@@ -22,4 +28,4 @@ def test_count302_multiqc():
 
 @pytest.mark.count310
 def test_count310_multiqc():
-    assert os.path.exists(os.path.join(test_output_path, 'multiqc_report.html'))
+    assert os.path.exists(os.path.join(test_output_path, 'multiqc_report.html'))
\ No newline at end of file

workflow/tests/test_versions.py

 #!/usr/bin/env python3
+#test_versions.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/develop/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd
@@ -26,4 +32,4 @@ def test_count302_versions():
 @pytest.mark.count310
 def test_count310_versions():
     assert os.path.exists(os.path.join(test_output_path, 'versions_mqc.yaml'))
-    assert os.path.exists(os.path.join(test_output_path, 'references_mqc.yaml'))
+    assert os.path.exists(os.path.join(test_output_path, 'references_mqc.yaml'))
\ No newline at end of file