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Commit 726b0d01 authored by Venkat Malladi's avatar Venkat Malladi
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Merge in changes.

parents 123c177c 6fddf146
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1 merge request!20Resolve "Use SampleIds/ Experiment Id as file names throughtout pipeline"
...@@ -12,13 +12,13 @@ user_configuration: ...@@ -12,13 +12,13 @@ user_configuration:
stage: unit stage: unit
script: script:
- pytest -m unit - pytest -m unit
-pytest -m unit --cov=./workflow/scripts
single_end_mouse: single_end_mouse:
stage: integration stage: integration
script: script:
- nextflow run workflow/main.nf -resume - nextflow run workflow/main.nf -resume
- pytest -m singleend - pytest -m singleend
- pytest --cov=./workflow/scripts
artifacts: artifacts:
expire_in: 2 days expire_in: 2 days
...@@ -27,7 +27,6 @@ paired_end_human: ...@@ -27,7 +27,6 @@ paired_end_human:
script: script:
- nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true -resume - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true -resume
- pytest -m pairedend - pytest -m pairedend
- pytest --cov=./workflow/scripts
artifacts: artifacts:
expire_in: 2 days expire_in: 2 days
...@@ -36,7 +35,6 @@ single_end_diff: ...@@ -36,7 +35,6 @@ single_end_diff:
script: script:
- nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' -resume - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' -resume
- pytest -m singlediff - pytest -m singlediff
- pytest --cov=./workflow/scripts
artifacts: artifacts:
expire_in: 2 days expire_in: 2 days
...@@ -45,6 +43,5 @@ paired_end_diff: ...@@ -45,6 +43,5 @@ paired_end_diff:
script: script:
- nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true -resume - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true -resume
- pytest -m paireddiff - pytest -m paireddiff
- pytest --cov=./workflow/scripts
artifacts: artifacts:
expire_in: 2 days expire_in: 2 days
...@@ -16,7 +16,7 @@ def test_annotate_peaks_singleend(): ...@@ -16,7 +16,7 @@ def test_annotate_peaks_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.chipseeker_upsetplot.pdf')) assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.chipseeker_upsetplot.pdf'))
annotation_file = test_output_path + 'ENCSR238SGC.chipseeker_annotation.csv' annotation_file = test_output_path + 'ENCSR238SGC.chipseeker_annotation.csv'
assert os.path.exists(annotation_file) assert os.path.exists(annotation_file)
assert utils.count_lines(annotation_file) == 152840 assert utils.count_lines(annotation_file) == 149820
@pytest.mark.pairedend @pytest.mark.pairedend
......
...@@ -12,7 +12,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \ ...@@ -12,7 +12,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.singleend @pytest.mark.singleend
def test_motif_search_singleend(): def test_motif_search_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.fa')) assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC_memechip', 'ENCSR238SGC.fa'))
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC_memechip', 'index.html')) assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC_memechip', 'index.html'))
peak_file_ENCSR238SGC = test_output_path + 'ENCSR238SGC.600.narrowPeak' peak_file_ENCSR238SGC = test_output_path + 'ENCSR238SGC.600.narrowPeak'
assert os.path.exists(peak_file_ENCSR238SGC) assert os.path.exists(peak_file_ENCSR238SGC)
...@@ -20,7 +20,7 @@ def test_motif_search_singleend(): ...@@ -20,7 +20,7 @@ def test_motif_search_singleend():
@pytest.mark.pairedend @pytest.mark.pairedend
def test_motif_search_pairedend(): def test_motif_search_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA.fa')) assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA_memechip', 'ENCSR729LGA.fa'))
assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA_memechip', 'index.html')) assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA_memechip', 'index.html'))
peak_file_ENCSR729LGA= test_output_path + 'ENCSR729LGA.600.narrowPeak' peak_file_ENCSR729LGA= test_output_path + 'ENCSR729LGA.600.narrowPeak'
assert os.path.exists(peak_file_ENCSR729LGA) assert os.path.exists(peak_file_ENCSR729LGA)
......
...@@ -9,20 +9,21 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \ ...@@ -9,20 +9,21 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.singleend @pytest.mark.singleend
def test_map_qc_singleend(): <<<<<<< HEAD
def test_cross_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCFF833BLU.cc.plot.pdf')) assert os.path.exists(os.path.join(test_output_path, 'ENCFF833BLU.cc.plot.pdf'))
qc_file = os.path.join(test_output_path,"ENCFF833BLU.cc.qc") qc_file = os.path.join(test_output_path,"ENCFF833BLU.cc.qc")
df_xcor = pd.read_csv(qc_file, sep="\t", header=None) df_xcor = pd.read_csv(qc_file, sep="\t", header=None)
assert df_xcor[2].iloc[0] == '190,200,210' assert df_xcor[2].iloc[0] == '190,200,210'
assert df_xcor[8].iloc[0] == 1.025906 assert df_xcor[8].iloc[0] == 1.025906
assert df_xcor[9].iloc[0] == 1.139671 assert round(df_xcor[9].iloc[0], 6) == 1.139671
@pytest.mark.pairedend @pytest.mark.pairedend
def test_map_qc_pairedend(): def test_cross_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.cc.plot.pdf')) assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.cc.plot.pdf'))
qc_file = os.path.join(test_output_path,"ENCLB568IYX.cc.qc") qc_file = os.path.join(test_output_path,"ENCLB568IYX.cc.qc")
df_xcor = pd.read_csv(qc_file, sep="\t", header=None) df_xcor = pd.read_csv(qc_file, sep="\t", header=None)
assert df_xcor[2].iloc[0] == '210,220,475' assert df_xcor[2].iloc[0] == '210,220,475'
assert df_xcor[8].iloc[0] == 1.062032 assert round(df_xcor[8].iloc[0],6) == 1.062032
assert df_xcor[9].iloc[0] == 3.737722 assert df_xcor[9].iloc[0] == 3.737722
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