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Commit a7adaad5 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
Browse files

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
parent e5695307
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......@@ -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
......@@ -6,7 +6,6 @@
#* --------------------------------------------------------------------------
#*
fastqs=($(ls *.fastq.gz))
design=$(ls *.csv)
sample=$(cat ${design} | tail -n +2 | cut -d ',' -f2)
......
#!/usr/bin/env python
#
# * --------------------------------------------------------------------------
# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/LICENSE.md)
# * --------------------------------------------------------------------------
#
'''Make header for HTML of references.'''
#generate_references.py
#*
#* --------------------------------------------------------------------------
#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/blob/develop/LICENSE)
#* --------------------------------------------------------------------------
#*
import argparse
import subprocess
......
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#generate_versions.py
#*
#* --------------------------------------------------------------------------
#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/blob/develop/LICENSE)
#* --------------------------------------------------------------------------
#*
'''Make YAML of software versions.'''
......@@ -15,8 +20,6 @@ For more details:
%(prog)s --help
'''
# SETTINGS
logger = logging.getLogger(__name__)
logger.addHandler(logging.NullHandler())
logger.propagate = False
......@@ -107,4 +110,4 @@ def main():
if __name__ == '__main__':
main()
main()
\ No newline at end of file
......@@ -34,4 +34,4 @@ name=$(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
#!/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
......@@ -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
#!/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
#!/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
#!/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
#!/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
#!/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
#!/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
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