def test_publish_qc_barcode_analysis(self):
"""publish_qc: barcode analysis outputs
"""
# Make an auto-process directory
mockdir = MockAnalysisDirFactory.bcl2fastq2(
'160621_K00879_0087_000000000-AGEW9',
'hiseq',
metadata={
"run_number": 87,
"source": "local",
"instrument_datestamp": "160621"
},
top_dir=self.dirn)
mockdir.create(no_project_dirs=True)
ap = AutoProcess(mockdir.dirn, settings=self.settings)
# Add processing and barcode analysis reports
UpdateAnalysisDir(ap).add_processing_report()
UpdateAnalysisDir(ap).add_barcode_analysis()
# Make a mock publication area
publication_dir = os.path.join(self.dirn, 'QC')
os.mkdir(publication_dir)
# Publish QC
publish_qc(ap, location=publication_dir)
# Check outputs
outputs = ("index.html", "processing_qc.html",
os.path.join("barcodes", "barcodes.report"),
os.path.join("barcodes", "barcodes.xls"),
os.path.join("barcodes", "barcodes.html"))
for item in outputs:
f = os.path.join(publication_dir,
"160621_K00879_0087_000000000-AGEW9_analysis",
item)
self.assertTrue(os.path.exists(f), "Missing %s" % f)
def test_publish_qc_with_cellranger_qc_multiple_lanes_subsets(self):
"""publish_qc: publish cellranger QC output (multiple subsets of lanes)
"""
# Make an auto-process directory
mockdir = MockAnalysisDirFactory.bcl2fastq2(
'160621_K00879_0087_000000000-AGEW9',
'hiseq',
metadata={
"run_number": 87,
"source": "local",
"instrument_datestamp": "160621"
},
top_dir=self.dirn)
mockdir.create(no_project_dirs=True)
ap = AutoProcess(mockdir.dirn, settings=self.settings)
# Add processing and cellranger QC reports
UpdateAnalysisDir(ap).add_processing_report()
UpdateAnalysisDir(ap).add_cellranger_qc_output(lanes="45")
UpdateAnalysisDir(ap).add_cellranger_qc_output(lanes="78")
# Make a mock publication area
publication_dir = os.path.join(self.dirn, 'QC')
os.mkdir(publication_dir)
# Publish
publish_qc(ap, location=publication_dir)
# Check outputs
outputs = [
"index.html", "processing_qc.html",
"cellranger_qc_summary_45.html", "cellranger_qc_summary_78.html"
]
# Do checks
for item in outputs:
f = os.path.join(publication_dir,
"160621_K00879_0087_000000000-AGEW9_analysis",
item)
self.assertTrue(os.path.exists(f), "Missing %s" % f)
def test_publish_qc_missing_destination(self):
"""publish_qc: raise exception if destination doesn't exist
"""
# Make an auto-process directory
mockdir = MockAnalysisDirFactory.bcl2fastq2(
'160621_K00879_0087_000000000-AGEW9',
'hiseq',
metadata={
"run_number": 87,
"source": "local",
"instrument_datestamp": "160621"
},
top_dir=self.dirn)
mockdir.create()
ap = AutoProcess(mockdir.dirn, settings=self.settings)
# Add processing report and QC outputs
UpdateAnalysisDir(ap).add_processing_report()
for project in ap.get_analysis_projects():
UpdateAnalysisProject(project).add_qc_outputs()
# Reference publication area which doesn't exist
publication_dir = os.path.join(self.dirn, 'QC')
self.assertFalse(os.path.exists(publication_dir))
# Publish
self.assertRaises(Exception, publish_qc, ap, location=publication_dir)
self.assertFalse(os.path.exists(publication_dir))
def test_publish_qc_with_project_missing_qc(self):
"""publish_qc: raises exception if project has missing QC
"""
# Make an auto-process directory
mockdir = MockAnalysisDirFactory.bcl2fastq2(
'160621_K00879_0087_000000000-AGEW9',
'hiseq',
metadata={
"run_number": 87,
"source": "local",
"instrument_datestamp": "160621"
},
top_dir=self.dirn)
mockdir.create()
ap = AutoProcess(mockdir.dirn, settings=self.settings)
# Add processing report
UpdateAnalysisDir(ap).add_processing_report()
# Add QC outputs for subset of projects
projects = ap.get_analysis_projects()[1:]
for project in projects:
UpdateAnalysisProject(project).add_qc_outputs()
# Make a mock publication area
publication_dir = os.path.join(self.dirn, 'QC')
os.mkdir(publication_dir)
# Publish
self.assertRaises(Exception, publish_qc, ap, location=publication_dir)
def test_publish_qc_with_projects_with_multiple_fastq_sets(self):
"""publish_qc: projects with multiple Fastq sets
"""
# Make an auto-process directory
mockdir = MockAnalysisDirFactory.bcl2fastq2(
'160621_K00879_0087_000000000-AGEW9',
'hiseq',
metadata={ "run_number": 87,
"source": "local",
"instrument_datestamp": "160621" },
top_dir=self.dirn)
mockdir.create()
ap = AutoProcess(mockdir.dirn)
# Add processing report and QC outputs
UpdateAnalysisDir(ap).add_processing_report()
for project in ap.get_analysis_projects():
UpdateAnalysisProject(project).add_qc_outputs()
# Add additional fastq set for first project
multi_fastqs_project = ap.get_analysis_projects()[0]
UpdateAnalysisProject(multi_fastqs_project).add_fastq_set(
"fastqs.extra",
("Alt1.r1.fastq.gz","Alt2.r1.fastq.gz"))
UpdateAnalysisProject(multi_fastqs_project).add_qc_outputs(
fastq_set="fastqs.extra",
qc_dir="qc.extra")
# Make a mock publication area
publication_dir = os.path.join(self.dirn,'QC')
os.mkdir(publication_dir)
# Publish
publish_qc(ap,location=publication_dir)
# Check outputs
outputs = ["index.html",
"processing_qc.html"]
for project in ap.get_analysis_projects():
# Standard QC outputs
project_qc = "qc_report.%s.%s" % (project.name,
os.path.basename(
ap.analysis_dir))
outputs.append(project_qc)
outputs.append("%s.zip" % project_qc)
outputs.append(os.path.join(project_qc,"qc_report.html"))
outputs.append(os.path.join(project_qc,"qc"))
# MultiQC output
outputs.append("multiqc_report.%s.html" % project.name)
# Additional QC for second fastq set in first project
project_qc = "qc.extra_report.%s.%s" % (multi_fastqs_project.name,
os.path.basename(
ap.analysis_dir))
outputs.append(project_qc)
outputs.append("%s.zip" % project_qc)
outputs.append(os.path.join(project_qc,"qc.extra_report.html"))
outputs.append(os.path.join(project_qc,"qc.extra"))
# MultiQC output
outputs.append("multiqc.extra_report.%s.html" %
multi_fastqs_project.name)
for item in outputs:
f = os.path.join(publication_dir,
"160621_K00879_0087_000000000-AGEW9_analysis",
item)
self.assertTrue(os.path.exists(f),"Missing %s" % f)
def test_clone_analysis_dir_copy_fastqs(self):
"""
clone: copies an analysis directory
"""
# Make a source analysis dir
analysis_dir = MockAnalysisDirFactory.bcl2fastq2(
"190116_M01234_0002_AXYZ123",
platform="miseq",
paired_end=True,
no_lane_splitting=False,
include_stats_files=True,
top_dir=self.dirn)
analysis_dir.create()
ap = AutoProcess(analysis_dir.dirn)
UpdateAnalysisDir(ap).add_processing_report()
ap.add_directory("primary_data/190116_M01234_0002_AXYZ123")
# Make a copy
clone_dir = os.path.join(self.dirn, "190116_M01234_0002_AXYZ123_copy")
self.assertFalse(os.path.exists(clone_dir))
clone(ap, clone_dir, copy_fastqs=True)
self.assertTrue(os.path.isdir(clone_dir))
# Check contents
for subdir in ('logs', 'ScriptCode'):
d = os.path.join(clone_dir, subdir)
self.assertTrue(os.path.isdir(d), "Missing '%s'" % subdir)
for filen in (
'SampleSheet.orig.csv',
'custom_SampleSheet.csv',
'auto_process.info',
'metadata.info',
'statistics.info',
'statistics_full.info',
'per_lane_statistics.info',
'per_lane_sample_stats.info',
'processing_qc.html',
):
f = os.path.join(clone_dir, filen)
self.assertTrue(os.path.isfile(f), "Missing '%s'" % filen)
# Check unaligned
unaligned = os.path.join(clone_dir, 'bcl2fastq')
self.assertTrue(os.path.isdir(unaligned))
# Check primary data
primary_data = os.path.join(clone_dir, 'primary_data',
'190116_M01234_0002_AXYZ123')
self.assertTrue(os.path.islink(primary_data))
# Check projects
for proj in ('AB', 'CDE', 'undetermined'):
d = os.path.join(clone_dir, proj)
self.assertTrue(os.path.isdir(d), "Missing '%s'" % proj)
# Check parameters
params = AnalysisDirParameters(
filen=os.path.join(clone_dir, 'auto_process.info'))
self.assertEqual(params.sample_sheet,
os.path.join(clone_dir, "custom_SampleSheet.csv"))
self.assertEqual(params.primary_data_dir,
os.path.join(clone_dir, "primary_data"))
def test_publish_qc_subset_of_projects(self):
"""publish_qc: only publish subset of projects
"""
# Make an auto-process directory
mockdir = MockAnalysisDirFactory.bcl2fastq2(
'160621_K00879_0087_000000000-AGEW9',
'hiseq',
metadata={ "run_number": 87,
"source": "local",
"instrument_datestamp": "160621" },
top_dir=self.dirn)
mockdir.create()
ap = AutoProcess(mockdir.dirn)
# Add processing report
UpdateAnalysisDir(ap).add_processing_report()
# Add QC outputs for subset of projects
projects = ap.get_analysis_projects()
missing_projects = projects[1:]
projects = projects[0:1]
for project in ap.get_analysis_projects():
UpdateAnalysisProject(project).add_qc_outputs()
# Make a mock publication area
publication_dir = os.path.join(self.dirn,'QC')
os.mkdir(publication_dir)
# Publish
publish_qc(ap,location=publication_dir,
projects="AB*")
# Check outputs
outputs = ["index.html",
"processing_qc.html"]
for project in projects:
# Standard QC outputs
project_qc = "qc_report.%s.%s" % (project.name,
os.path.basename(
ap.analysis_dir))
outputs.append(project_qc)
outputs.append("%s.zip" % project_qc)
outputs.append(os.path.join(project_qc,"qc_report.html"))
outputs.append(os.path.join(project_qc,"qc"))
# MultiQC output
outputs.append("multiqc_report.%s.html" % project.name)
for item in outputs:
f = os.path.join(publication_dir,
"160621_K00879_0087_000000000-AGEW9_analysis",
item)
self.assertTrue(os.path.exists(f),"Missing %s" % f)
# Check that missing projects weren't copied
for project in missing_projects:
self.assertFalse(os.path.exists(
os.path.join(publication_dir,
"160621_K00879_0087_000000000-AGEW9_analysis",
"qc_report.%s.%s" % (project.name,
os.path.basename(
ap.analysis_dir)))),
"%s exists in final dir, but shouldn't" %
project.name)
def test_publish_qc_with_icell8_outputs(self):
"""publish_qc: project with ICell8 QC outputs
"""
# Make an auto-process directory
mockdir = MockAnalysisDirFactory.bcl2fastq2(
'160621_K00879_0087_000000000-AGEW9',
'hiseq',
metadata={ "run_number": 87,
"source": "local",
"instrument_datestamp": "160621" },
top_dir=self.dirn)
mockdir.create()
ap = AutoProcess(mockdir.dirn)
# Add processing report and QC outputs
UpdateAnalysisDir(ap).add_processing_report()
projects = ap.get_analysis_projects()
for project in projects:
UpdateAnalysisProject(project).add_qc_outputs()
# Add ICell8 report for one project
icell8_project = projects[0]
UpdateAnalysisProject(icell8_project).add_icell8_outputs()
# Make a mock publication area
publication_dir = os.path.join(self.dirn,'QC')
os.mkdir(publication_dir)
# Publish
publish_qc(ap,location=publication_dir)
# Check outputs
outputs = ["index.html",
"processing_qc.html"]
for project in ap.get_analysis_projects():
# Standard QC outputs
project_qc = "qc_report.%s.%s" % (project.name,
os.path.basename(
ap.analysis_dir))
outputs.append(project_qc)
outputs.append("%s.zip" % project_qc)
outputs.append(os.path.join(project_qc,"qc_report.html"))
outputs.append(os.path.join(project_qc,"qc"))
# MultiQC output
outputs.append("multiqc_report.%s.html" % project.name)
# ICell8 outputs
icell8_dir = "icell8_processing.%s.%s" % (icell8_project.name,
os.path.basename(
ap.analysis_dir))
outputs.append(icell8_dir)
outputs.append("%s.zip" % icell8_dir)
outputs.append(os.path.join(icell8_dir,"icell8_processing_data"))
outputs.append(os.path.join(icell8_dir,"icell8_processing.html"))
outputs.append(os.path.join(icell8_dir,"stats"))
# Do checks
for item in outputs:
f = os.path.join(publication_dir,
"160621_K00879_0087_000000000-AGEW9_analysis",
item)
self.assertTrue(os.path.exists(f),"Missing %s" % f)
def test_publish_qc_with_projects_no_reports(self):
"""publish_qc: projects with all QC outputs but no reports
"""
# Make an auto-process directory
mockdir = MockAnalysisDirFactory.bcl2fastq2(
'160621_K00879_0087_000000000-AGEW9',
'hiseq',
metadata={
"run_number": 87,
"source": "local",
"instrument_datestamp": "160621"
},
top_dir=self.dirn)
mockdir.create()
ap = AutoProcess(mockdir.dirn, settings=self.settings)
# Add processing report and QC outputs
UpdateAnalysisDir(ap).add_processing_report()
for project in ap.get_analysis_projects():
UpdateAnalysisProject(project).add_qc_outputs()
# Remove the QC reports
for project in ap.get_analysis_projects():
qc_reports = []
qc_reports.append(
"qc_report.%s.%s.zip" %
(project.name, os.path.basename(ap.analysis_dir)))
qc_reports.append("qc_report.html")
qc_reports.append("multiqc_report.html")
for f in qc_reports:
os.remove(os.path.join(project.dirn, f))
# Make a mock multiqc
MockMultiQC.create(os.path.join(self.bin, "multiqc"))
os.environ['PATH'] = "%s:%s" % (self.bin, os.environ['PATH'])
# Make a mock publication area
publication_dir = os.path.join(self.dirn, 'QC')
os.mkdir(publication_dir)
# Publish
publish_qc(ap, location=publication_dir)
# Check outputs
outputs = ["index.html", "processing_qc.html"]
for project in ap.get_analysis_projects():
# Standard QC outputs
project_qc = "qc_report.%s.%s" % (
project.name, os.path.basename(ap.analysis_dir))
outputs.append(project_qc)
outputs.append("%s.zip" % project_qc)
outputs.append(os.path.join(project_qc, "qc_report.html"))
outputs.append(os.path.join(project_qc, "qc"))
for item in outputs:
f = os.path.join(publication_dir,
"160621_K00879_0087_000000000-AGEW9_analysis",
item)
self.assertTrue(os.path.exists(f), "Missing %s" % f)
def test_publish_qc_use_hierarchy(self):
"""publish_qc: publish using YEAR/PLATFORM hierarchy
"""
# Make an auto-process directory
mockdir = MockAnalysisDirFactory.bcl2fastq2(
'160621_K00879_0087_000000000-AGEW9',
'hiseq',
metadata={ "run_number": 87,
"source": "local",
"instrument_datestamp": "160621" },
top_dir=self.dirn)
mockdir.create()
ap = AutoProcess(mockdir.dirn)
# Add processing report and QC outputs
UpdateAnalysisDir(ap).add_processing_report()
for project in ap.get_analysis_projects():
UpdateAnalysisProject(project).add_qc_outputs()
# Make a mock publication area
publication_dir = os.path.join(self.dirn,'QC')
os.mkdir(publication_dir)
# Publish
publish_qc(ap,location=publication_dir,
use_hierarchy=True)
# Check outputs
final_dir = os.path.join(publication_dir,
"2016",
"hiseq")
self.assertTrue(os.path.exists(final_dir))
outputs = ["index.html",
"processing_qc.html"]
for project in ap.get_analysis_projects():
# Standard QC outputs
project_qc = "qc_report.%s.%s" % (project.name,
os.path.basename(
ap.analysis_dir))
outputs.append(project_qc)
outputs.append("%s.zip" % project_qc)
outputs.append(os.path.join(project_qc,"qc_report.html"))
outputs.append(os.path.join(project_qc,"qc"))
# MultiQC output
outputs.append("multiqc_report.%s.html" % project.name)
for item in outputs:
f = os.path.join(final_dir,
"160621_K00879_0087_000000000-AGEW9_analysis",
item)
self.assertTrue(os.path.exists(f),"Missing %s" % f)
def test_clone_fails_if_target_dir_exists(self):
"""
clone: raises an exception if target dir already exists
"""
# Make a source analysis dir
analysis_dir = MockAnalysisDirFactory.bcl2fastq2(
"190116_M01234_0002_AXYZ123",
platform="miseq",
paired_end=True,
no_lane_splitting=False,
include_stats_files=True,
top_dir=self.dirn)
analysis_dir.create()
ap = AutoProcess(analysis_dir.dirn)
UpdateAnalysisDir(ap).add_processing_report()
ap.add_directory("primary_data/190116_M01234_0002_AXYZ123")
# Make target dir
clone_dir = os.path.join(self.dirn, "190116_M01234_0002_AXYZ123_copy")
os.mkdir(clone_dir)
# Try to copy source dir
self.assertRaises(Exception, clone, ap, clone_dir)
def test_publish_qc_exclude_zip_files(self):
"""publish_qc: exclude ZIP files from publication
"""
# Make an auto-process directory
mockdir = MockAnalysisDirFactory.bcl2fastq2(
'160621_K00879_0087_000000000-AGEW9',
'hiseq',
metadata={
"run_number": 87,
"source": "local",
"instrument_datestamp": "160621"
},
top_dir=self.dirn)
mockdir.create()
ap = AutoProcess(mockdir.dirn, settings=self.settings)
# Add processing report and QC outputs
UpdateAnalysisDir(ap).add_processing_report()
projects = ap.get_analysis_projects()
for project in projects:
UpdateAnalysisProject(project).add_qc_outputs()
# Add ICell8 report for one project
icell8_project = projects[0]
UpdateAnalysisProject(icell8_project).add_icell8_outputs()
# Add cellranger count output for one project
tenxgenomics_project = projects[-1]
UpdateAnalysisProject(
tenxgenomics_project).add_cellranger_count_outputs()
# Make a mock publication area
publication_dir = os.path.join(self.dirn, 'QC')
os.mkdir(publication_dir)
# Publish
publish_qc(ap, location=publication_dir, exclude_zip_files=True)
# Check outputs
outputs = ["index.html", "processing_qc.html"]
zip_files = []
for project in ap.get_analysis_projects():
# Standard QC outputs
project_qc = "qc_report.%s.%s" % (
project.name, os.path.basename(ap.analysis_dir))
outputs.append(project_qc)
outputs.append(os.path.join(project_qc, "qc_report.html"))
outputs.append(os.path.join(project_qc, "qc"))
zip_files.append("%s.zip" % project_qc)
# ICell8 outputs
icell8_dir = "icell8_processing.%s.%s" % (
icell8_project.name, os.path.basename(ap.analysis_dir))
outputs.append(icell8_dir)
outputs.append(os.path.join(icell8_dir, "icell8_processing_data"))
outputs.append(os.path.join(icell8_dir, "icell8_processing.html"))
outputs.append(os.path.join(icell8_dir, "stats"))
zip_files.append("%s.zip" % icell8_dir)
# Cellranger count outputs
cellranger_count_dir = "cellranger_count_report.%s.%s" % (
tenxgenomics_project.name, os.path.basename(ap.analysis_dir))
outputs.append(cellranger_count_dir)
outputs.append(
os.path.join(cellranger_count_dir, "cellranger_count_report.html"))
outputs.append(os.path.join(cellranger_count_dir, "cellranger_count"))
for sample in tenxgenomics_project.samples:
outputs.append(
os.path.join(cellranger_count_dir, "cellranger_count",
sample.name, "outs", "web_summary.html"))
zip_files.append("%s.zip" % cellranger_count_dir)
# Do checks
for item in outputs:
f = os.path.join(publication_dir,
"160621_K00879_0087_000000000-AGEW9_analysis",
item)
self.assertTrue(os.path.exists(f), "Missing %s" % f)
for item in outputs:
f = os.path.join(publication_dir,
"160621_K00879_0087_000000000-AGEW9_analysis",
item)
self.assertTrue(os.path.exists(f), "Missing %s" % f)
# Check the ZIP files were excluded
for zip_file in zip_files:
self.assertFalse(
os.path.exists(
os.path.join(
publication_dir,
"160621_K00879_0087_000000000-AGEW9_analysis",
zip_file)),
"ZIP file '%s' exists, but shouldn't" % zip_file)
def test_publish_qc_with_cellranger_counts(self):
"""publish_qc: project with cellranger count output
"""
# Make an auto-process directory
mockdir = MockAnalysisDirFactory.bcl2fastq2(
'160621_K00879_0087_000000000-AGEW9',
'hiseq',
metadata={
"run_number": 87,
"source": "local",
"instrument_datestamp": "160621"
},
top_dir=self.dirn)
mockdir.create()
ap = AutoProcess(mockdir.dirn, settings=self.settings)
# Add processing and cellranger QC reports
UpdateAnalysisDir(ap).add_processing_report()
UpdateAnalysisDir(ap).add_cellranger_qc_output()
# Add QC outputs
projects = ap.get_analysis_projects()
for project in projects:
UpdateAnalysisProject(project).add_qc_outputs(
protocol="singlecell")
# Add cellranger count output for one project
tenxgenomics_project = projects[0]
UpdateAnalysisProject(
tenxgenomics_project).add_cellranger_count_outputs()
# Make a mock publication area
publication_dir = os.path.join(self.dirn, 'QC')
os.mkdir(publication_dir)
# Publish
publish_qc(ap, location=publication_dir)
# Check outputs
outputs = [
"index.html", "processing_qc.html", "cellranger_qc_summary.html"
]
for project in ap.get_analysis_projects():
# Standard QC outputs
project_qc = "qc_report.%s.%s" % (
project.name, os.path.basename(ap.analysis_dir))
outputs.append(project_qc)
outputs.append("%s.zip" % project_qc)
outputs.append(os.path.join(project_qc, "qc_report.html"))
outputs.append(os.path.join(project_qc, "qc"))
# Cellranger count outputs
cellranger_count_dir = "cellranger_count_report.%s.%s" % (
tenxgenomics_project.name, os.path.basename(ap.analysis_dir))
outputs.append(cellranger_count_dir)
outputs.append("%s.zip" % cellranger_count_dir)
outputs.append(
os.path.join(cellranger_count_dir, "cellranger_count_report.html"))
outputs.append(os.path.join(cellranger_count_dir, "cellranger_count"))
for sample in tenxgenomics_project.samples:
outputs.append(
os.path.join(cellranger_count_dir, "cellranger_count",
sample.name, "outs", "web_summary.html"))
# Do checks
for item in outputs:
f = os.path.join(publication_dir,
"160621_K00879_0087_000000000-AGEW9_analysis",
item)
self.assertTrue(os.path.exists(f), "Missing %s" % f)
# Do checks
for item in outputs:
f = os.path.join(publication_dir,
"160621_K00879_0087_000000000-AGEW9_analysis",
item)
self.assertTrue(os.path.exists(f), "Missing %s" % f)
def test_clone_analysis_dir_empty_params(self):
"""
clone: copies an analysis directory when parameter file is empty
"""
# Make a source analysis dir
analysis_dir = MockAnalysisDirFactory.bcl2fastq2(
"190116_M01234_0002_AXYZ123",
platform="miseq",
paired_end=True,
no_lane_splitting=False,
include_stats_files=True,
top_dir=self.dirn)
analysis_dir.create()
ap = AutoProcess(analysis_dir.dirn)
UpdateAnalysisDir(ap).add_processing_report()
ap.add_directory("primary_data/190116_M01234_0002_AXYZ123")
# Remove data from parameter file
parameter_file = ap.parameter_file
tmp_parameter_file = os.path.join(self.dirn, 'new_params.tmp')
del (ap)
with open(parameter_file, 'r') as fp:
with open(tmp_parameter_file, 'w') as fpp:
for line in fp:
line = "%s\t." % line.split('\t')[0]
fpp.write(line)
os.remove(parameter_file)
os.rename(tmp_parameter_file, parameter_file)
ap = AutoProcess(analysis_dir.dirn)
# Make a copy
clone_dir = os.path.join(self.dirn, "190116_M01234_0002_AXYZ123_copy")
self.assertFalse(os.path.exists(clone_dir))
clone(ap, clone_dir, exclude_projects=False)
self.assertTrue(os.path.isdir(clone_dir))
# Check contents
for subdir in ('logs', 'ScriptCode'):
d = os.path.join(clone_dir, subdir)
self.assertTrue(os.path.isdir(d), "Missing '%s'" % subdir)
for filen in (
'SampleSheet.orig.csv',
'custom_SampleSheet.csv',
'auto_process.info',
'metadata.info',
'statistics.info',
'statistics_full.info',
'per_lane_statistics.info',
'per_lane_sample_stats.info',
'processing_qc.html',
):
f = os.path.join(clone_dir, filen)
self.assertTrue(os.path.isfile(f), "Missing '%s'" % filen)
# Check unaligned
unaligned = os.path.join(clone_dir, 'bcl2fastq')
self.assertTrue(os.path.islink(unaligned))
# Check primary data
primary_data = os.path.join(clone_dir, 'primary_data',
'190116_M01234_0002_AXYZ123')
self.assertFalse(os.path.exists(primary_data))
# Check projects
for proj in ('AB', 'CDE', 'undetermined'):
d = os.path.join(clone_dir, proj)
self.assertTrue(os.path.exists(d), "Missing '%s'" % proj)
