def test_junoassembly_dryrun_wMetadata(self):
"""Testing the pipeline runs properly as a dry run when providing
a metadata file
"""
pathlib.Path('fake_dir_wsamples/missingsamp_1.fastq').unlink()
pathlib.Path('fake_dir_wsamples/missingsamp_2.fastq').unlink()
full_input_dir = pathlib.Path('fake_dir_wsamples').resolve()
pipeline_dry_run = juno_assembly.JunoAssemblyRun(
input_dir=full_input_dir,
metadata=str(full_input_dir.joinpath('fake_metadata.csv')),
output_dir=pathlib.Path('test_output'),
dryrun=True)
expected_sample_sheet = {
'sample1': {
'R1': str(full_input_dir.joinpath('sample1_R1.fastq')),
'R2': str(full_input_dir.joinpath('sample1_R2.fastq.gz')),
'genus': 'salmonella'
},
'sample2': {
'R1': str(full_input_dir.joinpath('sample2_R1_filt.fq')),
'R2': str(full_input_dir.joinpath('sample2_R2_filt.fq.gz')),
'genus': 'escherichia'
},
'1234': {
'R1': str(full_input_dir.joinpath('1234_R1.fastq.gz')),
'R2': str(full_input_dir.joinpath('1234_R2.fastq.gz')),
'genus': 'campylobacter'
}
}
self.assertTrue(pipeline_dry_run.successful_run,
'Exception raised when running a dryrun')
self.assertEqual(pipeline_dry_run.sample_dict, expected_sample_sheet,
pipeline_dry_run.sample_dict)
def test_junoassembly_dryrun_if_genus_provided(self):
"""Testing the pipeline runs properly as a dry run"""
input_dir = 'fake_dir_wsamples'
full_input_dir = pathlib.Path(input_dir).resolve()
pipeline_dry_run = juno_assembly.JunoAssemblyRun(
input_dir=input_dir,
metadata=None,
genus='salmonella',
output_dir=pathlib.Path('test_output'),
dryrun=True)
expected_sample_sheet = {
'sample1': {
'R1': str(full_input_dir.joinpath('sample1_R1.fastq')),
'R2': str(full_input_dir.joinpath('sample1_R2.fastq.gz')),
'genus': 'salmonella'
},
'sample2': {
'R1': str(full_input_dir.joinpath('sample2_R1_filt.fq')),
'R2': str(full_input_dir.joinpath('sample2_R2_filt.fq.gz')),
'genus': 'salmonella'
},
'1234': {
'R1': str(full_input_dir.joinpath('1234_R1.fastq.gz')),
'R2': str(full_input_dir.joinpath('1234_R2.fastq.gz')),
'genus': 'salmonella'
}
}
self.assertTrue(pipeline_dry_run.successful_run,
'Exception raised when running a dryrun')
self.assertEqual(
pipeline_dry_run.sample_dict, expected_sample_sheet, {
'pipeline': pipeline_dry_run.sample_dict,
'expected': expected_sample_sheet
})
def test_fails_with_empty_dir(self):
"""Testing the pipeline fails if input_dir is empty"""
with self.assertRaisesRegex(
ValueError,
'does not contain files that end with one of the expected extensions'
):
juno_assembly.JunoAssemblyRun(
input_dir='fake_empty_dir',
metadata=None,
output_dir=pathlib.Path('test_output'),
dryrun=True)
def test_junoassembly_fails_with_unsupported_genus(self):
"""Testing the pipeline runs properly as a dry run when providing a metadata file"""
with self.assertRaisesRegex(
ValueError, 'not supported. You can leave the "genus" empty'):
input_dir = 'fake_dir_wsamples'
full_input_dir = pathlib.Path(input_dir).resolve()
pipeline_dry_run = juno_assembly.JunoAssemblyRun(
input_dir=input_dir,
genus='fakegenus',
output_dir=pathlib.Path('test_output'),
dryrun=True)
def test_junoassembly_wdifferent_kmersize(self):
"""Testing the pipeline runs properly with real samples when providing
a metadata file
"""
output_dir = pathlib.Path('test_output_sing_prefix')
juno_assembly_run = juno_assembly.JunoAssemblyRun(
input_dir=
'/data/BioGrid/hernanda/test_data_per_pipeline/Juno_assembly',
metadata=None,
dryrun=False,
output_dir=output_dir,
run_in_container=True,
kmer_size=[21, 33, 55, 77],
prefix="sing_containers")
self.assertTrue(juno_assembly_run.successful_run,
'Exception raised when running Juno assembly')
def test_metadata_overwrites_genus(self):
"""Testing the pipeline runs properly as a dry run when providing
a metadata file. If both a genus and metadata are provided, the
metadata should overwrite the genus (unless sample not present)
"""
make_non_empty_file('fake_dir_wsamples/missingsamp_1.fastq')
make_non_empty_file('fake_dir_wsamples/missingsamp_2.fastq')
input_dir = 'fake_dir_wsamples'
full_input_dir = pathlib.Path(input_dir).resolve()
pipeline_dry_run = juno_assembly.JunoAssemblyRun(
input_dir=input_dir,
metadata='fake_dir_wsamples/fake_metadata.csv',
genus='salmonella',
output_dir=pathlib.Path('test_output'),
dryrun=True)
expected_sample_sheet = {
'sample1': {
'R1': str(full_input_dir.joinpath('sample1_R1.fastq')),
'R2': str(full_input_dir.joinpath('sample1_R2.fastq.gz')),
'genus': 'salmonella'
},
'sample2': {
'R1': str(full_input_dir.joinpath('sample2_R1_filt.fq')),
'R2': str(full_input_dir.joinpath('sample2_R2_filt.fq.gz')),
'genus': 'escherichia'
},
'1234': {
'R1': str(full_input_dir.joinpath('1234_R1.fastq.gz')),
'R2': str(full_input_dir.joinpath('1234_R2.fastq.gz')),
'genus': 'campylobacter'
},
'missingsamp': {
'R1': str(full_input_dir.joinpath('missingsamp_1.fastq')),
'R2': str(full_input_dir.joinpath('missingsamp_2.fastq')),
'genus': 'salmonella'
}
}
self.assertTrue(pipeline_dry_run.successful_run,
'Exception raised when running a dryrun')
self.assertEqual(
pipeline_dry_run.sample_dict, expected_sample_sheet, {
'pipeline': pipeline_dry_run.sample_dict,
'expected': expected_sample_sheet
})
def test_junoassembly_dryrun_if_metadata_incomplete(self):
"""Testing the pipeline runs properly as a dry run when providing a
metadata file and if a sample is not present in the metadata, then no genus
is assigned
"""
make_non_empty_file('fake_dir_wsamples/missingsamp_1.fastq')
make_non_empty_file('fake_dir_wsamples/missingsamp_2.fastq')
input_dir = 'fake_dir_wsamples'
full_input_dir = pathlib.Path(input_dir).resolve()
pipeline_dry_run = juno_assembly.JunoAssemblyRun(
input_dir=input_dir,
metadata='fake_dir_wsamples/fake_metadata.csv',
output_dir=pathlib.Path('test_output'),
dryrun=True)
expected_sample_sheet = {
'sample1': {
'R1': str(full_input_dir.joinpath('sample1_R1.fastq')),
'R2': str(full_input_dir.joinpath('sample1_R2.fastq.gz')),
'genus': 'salmonella'
},
'sample2': {
'R1': str(full_input_dir.joinpath('sample2_R1_filt.fq')),
'R2': str(full_input_dir.joinpath('sample2_R2_filt.fq.gz')),
'genus': 'escherichia'
},
'1234': {
'R1': str(full_input_dir.joinpath('1234_R1.fastq.gz')),
'R2': str(full_input_dir.joinpath('1234_R2.fastq.gz')),
'genus': 'campylobacter'
},
'missingsamp': {
'R1': str(full_input_dir.joinpath('missingsamp_1.fastq')),
'R2': str(full_input_dir.joinpath('missingsamp_2.fastq')),
'genus': None
}
}
self.assertTrue(pipeline_dry_run.successful_run,
'Exception raised when running a dryrun')
self.assertEqual(
pipeline_dry_run.sample_dict, expected_sample_sheet, {
'pipeline': pipeline_dry_run.sample_dict,
'expected': expected_sample_sheet
})
def test_junoassembly_dryrun_wrong_metadata_colnames(self):
"""
Tests whether a good error message is given if the metadata does not have the
expected column names
"""
with open('fake_dir_wsamples/fake_metadata2.csv',
mode='w') as metadata_file:
metadata_writer = csv.writer(metadata_file,
delimiter=',',
quotechar='"',
quoting=csv.QUOTE_MINIMAL)
metadata_writer.writerow(['Sample', 'Genus', 'Species'])
metadata_writer.writerow(['sample1', 'Salmonella', 'enterica'])
metadata_writer.writerow(['sample2', 'Escherichia', 'coli'])
metadata_writer.writerow(['1234', 'campylobacter', 'jejuni'])
full_input_dir = pathlib.Path('fake_dir_wsamples').resolve()
with self.assertRaisesRegex(
AssertionError,
'does not contain one or more of the expected column names'):
pipeline_dry_run = juno_assembly.JunoAssemblyRun(
input_dir=full_input_dir,
metadata=str(full_input_dir.joinpath('fake_metadata2.csv')),
output_dir=pathlib.Path('test_output'),
dryrun=True)
def test_junoassembly_wsingularity_prefix(self):
"""Testing the pipeline runs properly with real samples when providing
a metadata file
"""
output_dir = pathlib.Path('test_output_sing_prefix')
juno_assembly_run = juno_assembly.JunoAssemblyRun(
input_dir=
'/data/BioGrid/hernanda/test_data_per_pipeline/Juno_assembly',
metadata=None,
dryrun=False,
output_dir=output_dir,
run_in_container=True,
prefix="sing_containers")
expected_sample_sheet = {
'sample1': {
'R1':
'/data/BioGrid/hernanda/test_data_per_pipeline/Juno_assembly/sample1_S14_R1_001.fastq.gz',
'R2':
'/data/BioGrid/hernanda/test_data_per_pipeline/Juno_assembly/sample1_S14_R2_001.fastq.gz',
'genus': None
},
'sample2': {
'R1':
'/data/BioGrid/hernanda/test_data_per_pipeline/Juno_assembly/sample2_R1.fastq.gz',
'R2':
'/data/BioGrid/hernanda/test_data_per_pipeline/Juno_assembly/sample2_R2.fastq.gz',
'genus': None
},
'sample3': {
'R1':
'/data/BioGrid/hernanda/test_data_per_pipeline/Juno_assembly/sample3_R1_001.fastq.gz',
'R2':
'/data/BioGrid/hernanda/test_data_per_pipeline/Juno_assembly/sample3_R2_001.fastq.gz',
'genus': None
},
'sample4': {
'R1':
'/data/BioGrid/hernanda/test_data_per_pipeline/Juno_assembly/sample4_R1.fastq.gz',
'R2':
'/data/BioGrid/hernanda/test_data_per_pipeline/Juno_assembly/sample4_R2.fastq.gz',
'genus': None
}
}
self.assertEqual(juno_assembly_run.sample_dict, expected_sample_sheet,
juno_assembly_run.sample_dict)
self.assertTrue(juno_assembly_run.successful_run,
'Exception raised when running Juno assembly')
self.assertTrue(
output_dir.joinpath('multiqc', 'multiqc.html').exists())
self.assertTrue(
output_dir.joinpath('identify_species',
'top1_species_multireport.csv').exists())
self.assertTrue(
output_dir.joinpath('audit_trail', 'log_git.yaml').exists())
self.assertTrue(
output_dir.joinpath('audit_trail', 'log_pipeline.yaml').exists())
self.assertTrue(
output_dir.joinpath('audit_trail', 'log_conda.txt').exists())
self.assertTrue(
output_dir.joinpath('audit_trail',
'juno_assembly_report.html').exists())
self.assertTrue(
output_dir.joinpath('audit_trail', 'sample_sheet.yaml').exists())
self.assertTrue(
output_dir.joinpath('audit_trail',
'user_parameters.yaml').exists())