Commit 5055cccb authored by Venkat Malladi's avatar Venkat Malladi
Browse files

Test data for single control single replicate.

parent ca3e17e3
Pipeline #5971 canceled with stages
in 6 minutes and 5 seconds
......@@ -14,7 +14,6 @@ stages:
user_configuration:
stage: unit
script:
- pytest -m unit
- pytest -m unit --cov=./workflow/scripts
astrocyte:
......@@ -51,7 +50,8 @@ single_end_single_control:
- master
script:
- nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_single_contol_SE.txt" --genome 'GRCh38' --pairedEnd false --astrocyte false
- pytest -m singlecontrol
single_end_diff:
stage: multiple
only:
......
sample_id experiment_id biosample factor treatment replicate control_id fastq_read1
ENCLB497XZB ENCSR000DXB Panc1 H3K4me3 None 1 ENCLB304SBJ ENCFF001GBW.fastq.gz
ENCLB414AAH ENCSR000DXB Panc1 H3K4me3 None 2 ENCLB304SBJ ENCFF001GBV.fastq.gz
ENCLB304SBJ ENCSR000DXC Panc1 Control None 1 ENCLB304SBJ ENCFF001HWJ.fastq.gz
......@@ -45,3 +45,9 @@ def test_overlap_peaks_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA.rejected.narrowPeak'))
peak_file = test_output_path + 'ENCSR729LGA.replicated.narrowPeak'
assert utils.count_lines(peak_file) >= 25657
@pytest.mark.singlecontrol
def test_overlap_peaks_singlecontrol():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR000DXB.rejected.narrowPeak'))
peak_file = test_output_path + 'ENCSR000DXB.replicated.narrowPeak'
assert utils.count_lines(peak_file) >= 35097
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