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Commit a32879db authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Update pytests

parent 14b8fc1d
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2 merge requests!68Develop,!67Resolve "Change Single Read to Single End for submitted endness"
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.gitlab-ci.yml
+ 7
− 7
View file @ a32879db
......@@ -666,7 +666,7 @@ integration_se:
- ulimit -a
- nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-1ZX4 --source staging --upload true -with-dag dag.png --dev false --ci true -with-report ./SE_report.html
- find . -type f -name "multiqc_data.json" -exec cp {} ./SE_multiqc_data.json \;
- pytest -m completionIntegration_se
- pytest -m completion("SE_multiqc_data.json")
artifacts:
name: "$CI_JOB_NAME"
when: always
......@@ -691,7 +691,7 @@ integration_pe:
- ulimit -a
- nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA --source staging --upload true -with-dag dag.png --dev false --ci true -with-report ./PE_report.html
- find . -type f -name "multiqc_data.json" -exec cp {} ./PE_multiqc_data.json \;
- pytest -m completionIntegration_pe
- pytest -m completion("PE_multiqc_data.json")
artifacts:
name: "$CI_JOB_NAME"
when: always
......@@ -793,7 +793,7 @@ override_inputBag:
- ulimit -a
- nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --source staging --inputBagForce ./test_data/bag/Q-Y5F6_inputBag_xxxxxxxx.zip --upload false --dev false --ci true -with-report ./inputBagOverride_report.html
- find . -type f -name "multiqc_data.json" -exec cp {} ./inputBagOverride_PE_multiqc_data.json \;
- pytest -m completionOverride_inputBag
- pytest -m completion("inputBagOverride_PE_multiqc_data.json")
artifacts:
name: "$CI_JOB_NAME"
when: always
......@@ -816,7 +816,7 @@ override_fastq:
- ulimit -a
- nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --source staging --fastqsForce './test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz' --upload false --dev false --ci true -with-report ./fastqOverride_report.html
- find . -type f -name "multiqc_data.json" -exec cp {} ./fastqOverride_PE_multiqc_data.json \;
- pytest -m completionOverride_fastq
- pytest -m completion("fastqOverride_PE_multiqc_data.json")
artifacts:
name: "$CI_JOB_NAME"
when: always
......@@ -839,7 +839,7 @@ override_species:
- ulimit -a
- nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ER --source staging --speciesForce 'Homo sapiens' --upload false --dev false --ci true -with-report ./speciesOverride_report.html
- find . -type f -name "multiqc_data.json" -exec cp {} ./speciesOverride_PE_multiqc_data.json \;
- pytest -m completionOverride_spike
- pytest -m completion("speciesOverride_PE_multiqc_data.json")
artifacts:
name: "$CI_JOB_NAME"
when: always
......@@ -862,7 +862,7 @@ override_stranded:
- ulimit -a
- nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ER --source staging --strandedForce unstranded --upload false --dev false --ci true -with-report ./strandedOverride_report.html
- find . -type f -name "multiqc_data.json" -exec cp {} ./strandedOverride_PE_multiqc_data.json \;
- pytest -m completionOverride_stranded
- pytest -m completion("strandedOverride_PE_multiqc_data.json")
artifacts:
name: "$CI_JOB_NAME"
when: always
......@@ -885,7 +885,7 @@ override_spike:
- ulimit -a
- nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ER --source staging --spikeForce t --upload false --dev false --ci true -with-report ./spikeOverride_report.html
- find . -type f -name "multiqc_data.json" -exec cp {} ./spikeOverride_PE_multiqc_data.json \;
- pytest -m completionOverride_spike
- pytest -m completion("spikedOverride_PE_multiqc_data.json")
artifacts:
name: "$CI_JOB_NAME"
when: always
......
workflow/tests/test_alignReads.py
+ 7
− 7
View file @ a32879db
......@@ -5,25 +5,25 @@ import pandas as pd
import os
import utils
data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../../'
@pytest.mark.alignData
def test_alignData_se():
assert os.path.exists(os.path.join(
data_output_path, 'Q-Y5F6_1M.se.unal.gz'))
test_output_path, 'Q-Y5F6_1M.se.unal.gz'))
assert os.path.exists(os.path.join(
data_output_path, 'Q-Y5F6_1M.se.sorted.bam'))
test_output_path, 'Q-Y5F6_1M.se.sorted.bam'))
assert os.path.exists(os.path.join(
data_output_path, 'Q-Y5F6_1M.se.sorted.bam.bai'))
test_output_path, 'Q-Y5F6_1M.se.sorted.bam.bai'))
@pytest.mark.alignData
def test_alignData_pe():
assert os.path.exists(os.path.join(
data_output_path, 'Q-Y5F6_1M.pe.unal.gz'))
test_output_path, 'Q-Y5F6_1M.pe.unal.gz'))
assert os.path.exists(os.path.join(
data_output_path, 'Q-Y5F6_1M.pe.sorted.bam'))
test_output_path, 'Q-Y5F6_1M.pe.sorted.bam'))
assert os.path.exists(os.path.join(
data_output_path, 'Q-Y5F6_1M.pe.sorted.bam.bai'))
test_output_path, 'Q-Y5F6_1M.pe.sorted.bam.bai'))
workflow/tests/test_completion.py
+ 3
− 39
View file @ a32879db
......@@ -10,43 +10,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../../'
@pytest.mark.completionIntegration_se
def test_multiqc():
@pytest.mark.completion
def test_multiqc(file_name):
assert os.path.exists(os.path.join(
test_output_path, 'SE_multiqc_data.json'))
@pytest.mark.completionIntegration_pe
def test_multiqc():
assert os.path.exists(os.path.join(
test_output_path, 'PE_multiqc_data.json'))
@pytest.mark.completionOverride_inputBag
def test_multiqc():
assert os.path.exists(os.path.join(
test_output_path, 'inputBagOverride_PE_multiqc_data.json'))
@pytest.mark.completionOverride_fastq
def test_multiqc():
assert os.path.exists(os.path.join(
test_output_path, 'fastqOverride_PE_multiqc_data.json'))
@pytest.mark.completionOverride_species
def test_multiqc():
assert os.path.exists(os.path.join(
test_output_path, 'speciesOverride_PE_multiqc_data.json'))
@pytest.mark.completionOverride_stranded
def test_multiqc():
assert os.path.exists(os.path.join(
test_output_path, 'strandedOverride_PE_multiqc_data.json'))
@pytest.mark.completionOverride_spike
def test_multiqc():
assert os.path.exists(os.path.join(
test_output_path, 'spikeOverride_PE_multiqc_data.json'))
\ No newline at end of file
test_output_path, file_name))
\ No newline at end of file
workflow/tests/test_dedupReads.py
+ 9
− 9
View file @ a32879db
......@@ -5,25 +5,25 @@ import pandas as pd
import os
import utils
data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../../'
@pytest.mark.dedupData
def test_dedupData():
assert os.path.exists(os.path.join(
data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.bam'))
test_output_path, 'Q-Y5F6_1M.se.sorted.deduped.bam'))
assert os.path.exists(os.path.join(
data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.bam.bai'))
test_output_path, 'Q-Y5F6_1M.se.sorted.deduped.bam.bai'))
assert os.path.exists(os.path.join(
data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chr8.bam'))
test_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chr8.bam'))
assert os.path.exists(os.path.join(
data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chr8.bam.bai'))
test_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chr8.bam.bai'))
assert os.path.exists(os.path.join(
data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chr4.bam'))
test_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chr4.bam'))
assert os.path.exists(os.path.join(
data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chr4.bam.bai'))
test_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chr4.bam.bai'))
assert os.path.exists(os.path.join(
data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chrY.bam'))
test_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chrY.bam'))
assert os.path.exists(os.path.join(
data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chrY.bam.bai'))
test_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chrY.bam.bai'))
workflow/tests/test_makeBigWig.py
+ 2
− 2
View file @ a32879db
......@@ -5,10 +5,10 @@ import pandas as pd
import os
import utils
data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../../'
@pytest.mark.makeBigWig
def test_makeBigWig():
assert os.path.exists(os.path.join(data_output_path, 'Q-Y5F6_1M.se.bw'))
assert os.path.exists(os.path.join(test_output_path, 'Q-Y5F6_1M.se.bw'))
workflow/tests/test_makeFeatureCounts.py
+ 4
− 4
View file @ a32879db
......@@ -5,15 +5,15 @@ import pandas as pd
import os
import utils
data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../../'
@pytest.mark.makeFeatureCounts
def test_makeFeatureCounts():
assert os.path.exists(os.path.join(
data_output_path, 'Q-Y5F6_1M.se_countData'))
test_output_path, 'Q-Y5F6_1M.se_countData'))
assert os.path.exists(os.path.join(
data_output_path, 'Q-Y5F6_1M.se.countTable.csv'))
test_output_path, 'Q-Y5F6_1M.se.countTable.csv'))
assert os.path.exists(os.path.join(
data_output_path, 'Q-Y5F6_1M.se_tpmTable.csv'))
test_output_path, 'Q-Y5F6_1M.se_tpmTable.csv'))
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