Update workflow/scripts/generate_references.py,...

Update workflow/scripts/generate_references.py, workflow/scripts/generate_versions.py, workflow/scripts/versions_fastqc.sh, workflow/tests/test_check_design.py, workflow/scripts/countDesign.sh, workflow/tests/test_fastqc.py, workflow/tests/test_mkfastq.py, workflow/tests/test_multiqc.py, workflow/tests/test_untarBCL.py, workflow/tests/test_versions.py, workflow/scripts/versions_mkfastq.sh, workflow/scripts/untarBCL.sh, workflow/scripts/check_design.py files

workflow/scripts/check_design.py

@@ -6,8 +6,6 @@
 #* --------------------------------------------------------------------------
 #*
 
-'''Check if design file is correctly formatted and matches files list.'''
-
 import argparse
 import logging
 import pandas as pd
@@ -17,8 +15,6 @@ For more details:
         %(prog)s --help
 '''
 
-# SETTINGS
-
 logger = logging.getLogger(__name__)
 logger.addHandler(logging.NullHandler())
 logger.propagate = False
@@ -79,4 +75,4 @@ 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/countDesign.sh

@@ -6,7 +6,6 @@
 #* --------------------------------------------------------------------------
 #*
 
-
 fastqs=($(ls *.fastq.gz))
 design=$(ls *.csv)
 sample=$(cat ${design} | tail -n +2 | cut -d ',' -f2)

workflow/scripts/generate_references.py

 #!/usr/bin/env python
-
-#
-# * --------------------------------------------------------------------------
-# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/LICENSE.md)
-# * --------------------------------------------------------------------------
-#
-
-'''Make header for HTML of references.'''
+#generate_references.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/blob/develop/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import argparse
 import subprocess

workflow/scripts/generate_versions.py

 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
+#generate_versions.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/blob/develop/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 '''Make YAML of software versions.'''
 
@@ -15,8 +20,6 @@ For more details:
         %(prog)s --help
 '''
 
-# SETTINGS
-
 logger = logging.getLogger(__name__)
 logger.addHandler(logging.NullHandler())
 logger.propagate = False
@@ -107,4 +110,4 @@ def main():
 
 
 if __name__ == '__main__':
-    main()
+    main()
\ No newline at end of file

workflow/scripts/untarBCL.sh

@@ -34,4 +34,4 @@ name=$(echo ${tar} | rev | cut -f1 -d '.' | rev)
 if [ "${name}" == "gz" ]; then 
   tar -xvf ${tar} -I pigz
   else tar -xvf ${tar}
-fi
+fi
\ No newline at end of file

workflow/scripts/versions_fastqc.sh

 #!/bin/bash
+#versions_fastqc.sh
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/blob/develop/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
-fastqc --version | grep 'FastQC v' | sed -n -e 's/^FastQC v//p' > version_fastqc.txt  
+fastqc --version | grep 'FastQC v' | sed -n -e 's/^FastQC v//p' > version_fastqc.txt  
\ No newline at end of file

workflow/scripts/versions_mkfastq.sh

@@ -7,4 +7,4 @@
 #*
 
 cellranger mkfastq --version | grep 'cellranger mkfastq ' | sed 's/.*(\(.*\))/\1/' > version_cellranger.mkfastq.txt
-bcl2fastq --version |& grep 'bcl2fastq v' | sed -n -e 's/^bcl2fastq v//p' > version_bcl2fastq.txt  
+bcl2fastq --version |& grep 'bcl2fastq v' | sed -n -e 's/^bcl2fastq v//p' > version_bcl2fastq.txt  
\ 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_mkfastq/blob/develop/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd
@@ -14,4 +20,4 @@ def test_simple1_design():
 
 @pytest.mark.simple2
 def test_simple2_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_fastqc.py

 #!/usr/bin/env python3
+#test_fastq.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/blob/develop/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd
@@ -15,4 +21,4 @@ def test_simple1_fastqc():
 @pytest.mark.simple2
 def test_simple2_fastqc():
     assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0-1'))
-    assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0-2'))
+    assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0-2'))
\ No newline at end of file

workflow/tests/test_mkfastq.py

 #!/usr/bin/env python3
+#test_mkfastq.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/blob/develop/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd
@@ -15,4 +21,4 @@ def test_simple1_mkfastq():
 @pytest.mark.simple2
 def test_simple2_mkfastq():
     assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0-1', 'outs'))
-    assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0-2', 'outs'))
+    assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0-2', '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_mkfastq/blob/develop/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd
@@ -14,4 +20,4 @@ def test_simple1_multiqc():
 
 @pytest.mark.simple2
 def test_simple2_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_untarBCL.py

 #!/usr/bin/env python3
+#test_untarBCL.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/blob/develop/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd
@@ -15,4 +21,4 @@ def test_simple1_untarBCL():
 @pytest.mark.simple2
 def test_simple2_untarBCL():
     assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0-1', 'RTAComplete.txt'))
-    assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0-2', 'RTAComplete.txt'))
+    assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0-2', 'RTAComplete.txt'))
\ 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_mkfastq/blob/develop/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd
@@ -16,4 +22,4 @@ def test_simple1_versions():
 @pytest.mark.simple2
 def test_simple2_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