def test_get_samplesheet(self):
"""Locate the samplesheet in a folder
"""
# Work in a separate subdirectory
subdir = os.path.join(self.rootdir,"test_get_samplesheet")
os.mkdir(subdir)
# Create a few random files and folders and assert that they are not returned
suffixes = [".csv","",""]
for n in range(3):
os.mkdir(os.path.join(subdir,''.join(random.choice(string.ascii_uppercase) for x in range(5))))
fh, _ = tempfile.mkstemp(dir=subdir, suffix=suffixes[n])
os.close(fh)
self.assertIsNone(IlluminaRun.get_samplesheet(subdir),
"Getting non-existing samplesheet did not return None")
# Create a SampleSheet.csv and a [FCID].csv file and assert that they are
# returned with a preference for the [FCID].csv file
fcid = td.generate_fc_barcode()
fcdir = os.path.join(subdir,td.generate_run_id(fc_barcode=fcid))
os.mkdir(fcdir)
ss = [os.path.join(fcdir,"SampleSheet.csv"),
os.path.join(fcdir,"{}.csv".format(fcid))]
for s in ss:
utils.touch_file(s)
self.assertEqual(s,IlluminaRun.get_samplesheet(fcdir),
"Did not get existing {}".format(os.path.basename(s)))
shutil.rmtree(subdir)
def setUp(self):
self.rootdir = tempfile.mkdtemp(prefix="test_illumina_run_")
# Create a fcdir
self.exp_fcid = td.generate_fc_barcode()
self.exp_fcdir = os.path.join(
self.rootdir, td.generate_run_id(fc_barcode=self.exp_fcid))
os.mkdir(self.exp_fcdir)
# Create multiple sequence read directories
self.exp_seqdir = [
os.path.join(self.exp_fcdir, "Unaligned"),
os.path.join(self.exp_fcdir, "Unaligned_L6"),
os.path.join(self.exp_fcdir, "Unaligned_L8")
]
for d in self.exp_seqdir:
os.mkdir(d)
# Create directories for undetermined indices reads
self.exp_unmatched_directory = [
os.path.join(d, "Undetermined_indices")
for d in self.exp_seqdir[:-1]
]
for d in self.exp_unmatched_directory:
os.mkdir(d)
# Create basecall stats directories
self.exp_basecall_stats = [
os.path.join(d, "Basecall_Stats_{}".format(self.exp_fcid))
for d in self.exp_seqdir[1:]
]
for d in self.exp_basecall_stats:
os.mkdir(d)
self.run = IlluminaRun(self.exp_fcdir)
def setUp(self):
self.rootdir = tempfile.mkdtemp(prefix="test_illumina_run_")
# Create a fcdir
self.exp_fcid = td.generate_fc_barcode()
self.exp_fcdir = os.path.join(self.rootdir,td.generate_run_id(fc_barcode=self.exp_fcid))
os.mkdir(self.exp_fcdir)
# Create multiple sequence read directories
self.exp_seqdir = [os.path.join(self.exp_fcdir,"Unaligned"),
os.path.join(self.exp_fcdir,"Unaligned_L6"),
os.path.join(self.exp_fcdir,"Unaligned_L8")]
for d in self.exp_seqdir:
os.mkdir(d)
# Create directories for undetermined indices reads
self.exp_unmatched_directory = [os.path.join(d,"Undetermined_indices") for d in self.exp_seqdir[:-1]]
for d in self.exp_unmatched_directory:
os.mkdir(d)
# Create basecall stats directories
self.exp_basecall_stats = [os.path.join(d,"Basecall_Stats_{}".format(self.exp_fcid)) for d in self.exp_seqdir[1:]]
for d in self.exp_basecall_stats:
os.mkdir(d)
self.run = IlluminaRun(self.exp_fcdir)
def test_get_samplesheet(self):
"""Locate the samplesheet in a folder
"""
# Work in a separate subdirectory
subdir = os.path.join(self.rootdir, "test_get_samplesheet")
os.mkdir(subdir)
# Create a few random files and folders and assert that they are not returned
suffixes = [".csv", "", ""]
for n in range(3):
os.mkdir(
os.path.join(
subdir, ''.join(
random.choice(string.ascii_uppercase)
for x in range(5))))
fh, _ = tempfile.mkstemp(dir=subdir, suffix=suffixes[n])
os.close(fh)
self.assertIsNone(
IlluminaRun.get_samplesheet(subdir),
"Getting non-existing samplesheet did not return None")
# Create a SampleSheet.csv and a [FCID].csv file and assert that they are
# returned with a preference for the [FCID].csv file
fcid = td.generate_fc_barcode()
fcdir = os.path.join(subdir, td.generate_run_id(fc_barcode=fcid))
os.mkdir(fcdir)
ss = [
os.path.join(fcdir, "SampleSheet.csv"),
os.path.join(fcdir, "{}.csv".format(fcid))
]
for s in ss:
utils.touch_file(s)
self.assertEqual(
s, IlluminaRun.get_samplesheet(fcdir),
"Did not get existing {}".format(os.path.basename(s)))
shutil.rmtree(subdir)
def test_get_flowcell(self):
"""Get flowcell from analysis directory
"""
# Work in a separate subdirectory
subdir = os.path.join(self.rootdir, "test_get_flowcell")
os.mkdir(subdir)
# Create some folders
fc_dirs = []
for i in range(3):
fc_dirs.append(
tempfile.mkdtemp(suffix="{}_fc_dir".format(i), dir=subdir))
# Assert nothing is returned for non-existing flowcell
self.assertListEqual(
IlluminaRun.get_flowcell(subdir, 'flowcell_id'), [],
"Nothing should be returned for a non-existing flowcell id")
# Assert that the correct folders are returned for exact matches
for fc_dir in fc_dirs:
self.assertListEqual(
[fc_dir],
IlluminaRun.get_flowcell(subdir, os.path.basename(fc_dir)),
"Did not return the correct folder for exact match")
# Assert that an empty match returns all folders
self.assertListEqual(
sorted(fc_dirs), sorted(IlluminaRun.get_flowcell(subdir)),
"Did not return the correct folders for empty matches")
# Assert that a partial match is resolved to the correct folder
self.assertListEqual(
[fc_dirs[-1]],
IlluminaRun.get_flowcell(subdir, "{}_fc_dir".format(
str(len(fc_dirs) - 1))),
"Did not return the correct folder for partial match")
# Assert that an ambiguous match returns the matching folders
self.assertListEqual(
sorted(fc_dirs),
sorted(IlluminaRun.get_flowcell(subdir, "_fc_dir")),
"Did not return the correct folders for ambiguous matches")
# Assert that the correct folder is returned for an exact match that matches ambiguously when allowing wildcards
ambig_dir = os.path.join(subdir, "_fc_dir")
utils.safe_makedir(ambig_dir)
self.assertListEqual(
[ambig_dir],
sorted(
IlluminaRun.get_flowcell(subdir, os.path.basename(ambig_dir))),
"Did not return the correct folder for specific non-wildcard match"
)
shutil.rmtree(subdir)
def test_get_flowcell(self):
"""Get flowcell from analysis directory
"""
# Work in a separate subdirectory
subdir = os.path.join(self.rootdir,"test_get_flowcell")
os.mkdir(subdir)
# Create some folders
fc_dirs = []
for i in range(3):
fc_dirs.append(tempfile.mkdtemp(suffix="{}_fc_dir".format(i), dir=subdir))
# Assert nothing is returned for non-existing flowcell
self.assertListEqual(IlluminaRun.get_flowcell(subdir,'flowcell_id'),
[],
"Nothing should be returned for a non-existing flowcell id")
# Assert that the correct folders are returned for exact matches
for fc_dir in fc_dirs:
self.assertListEqual([fc_dir],
IlluminaRun.get_flowcell(subdir,os.path.basename(fc_dir)),
"Did not return the correct folder for exact match")
# Assert that an empty match returns all folders
self.assertListEqual(sorted(fc_dirs),
sorted(IlluminaRun.get_flowcell(subdir)),
"Did not return the correct folders for empty matches")
# Assert that a partial match is resolved to the correct folder
self.assertListEqual([fc_dirs[-1]],
IlluminaRun.get_flowcell(subdir,"{}_fc_dir".format(str(len(fc_dirs)-1))),
"Did not return the correct folder for partial match")
# Assert that an ambiguous match returns the matching folders
self.assertListEqual(sorted(fc_dirs),
sorted(IlluminaRun.get_flowcell(subdir,"_fc_dir")),
"Did not return the correct folders for ambiguous matches")
# Assert that the correct folder is returned for an exact match that matches ambiguously when allowing wildcards
ambig_dir = os.path.join(subdir,"_fc_dir")
utils.safe_makedir(ambig_dir)
self.assertListEqual([ambig_dir],
sorted(IlluminaRun.get_flowcell(subdir,os.path.basename(ambig_dir))),
"Did not return the correct folder for specific non-wildcard match")
shutil.rmtree(subdir)
class TestIlluminaRun(unittest.TestCase):
def setUp(self):
self.rootdir = tempfile.mkdtemp(prefix="test_illumina_run_")
# Create a fcdir
self.exp_fcid = td.generate_fc_barcode()
self.exp_fcdir = os.path.join(self.rootdir,td.generate_run_id(fc_barcode=self.exp_fcid))
os.mkdir(self.exp_fcdir)
# Create multiple sequence read directories
self.exp_seqdir = [os.path.join(self.exp_fcdir,"Unaligned"),
os.path.join(self.exp_fcdir,"Unaligned_L6"),
os.path.join(self.exp_fcdir,"Unaligned_L8")]
for d in self.exp_seqdir:
os.mkdir(d)
# Create directories for undetermined indices reads
self.exp_unmatched_directory = [os.path.join(d,"Undetermined_indices") for d in self.exp_seqdir[:-1]]
for d in self.exp_unmatched_directory:
os.mkdir(d)
# Create basecall stats directories
self.exp_basecall_stats = [os.path.join(d,"Basecall_Stats_{}".format(self.exp_fcid)) for d in self.exp_seqdir[1:]]
for d in self.exp_basecall_stats:
os.mkdir(d)
self.run = IlluminaRun(self.exp_fcdir)
def tearDown(self):
shutil.rmtree(self.rootdir)
def test_map_index_name(self):
"""Map index sequences to names
"""
# Some test cases
from scilifelab.illumina.index_definitions import BASIC_LOOKUP
random_keys = [BASIC_LOOKUP.keys()[random.randint(0,len(BASIC_LOOKUP.keys())-1)] for n in xrange(25)]
for name in random_keys:
self.assertIn(name,map_index_name(BASIC_LOOKUP[name],0),
"Exact mapping did not return expected index name")
def test_get_flowcell(self):
"""Get flowcell from analysis directory
"""
# Work in a separate subdirectory
subdir = os.path.join(self.rootdir,"test_get_flowcell")
os.mkdir(subdir)
# Create some folders
fc_dirs = []
for i in range(3):
fc_dirs.append(tempfile.mkdtemp(suffix="{}_fc_dir".format(i), dir=subdir))
# Assert nothing is returned for non-existing flowcell
self.assertListEqual(IlluminaRun.get_flowcell(subdir,'flowcell_id'),
[],
"Nothing should be returned for a non-existing flowcell id")
# Assert that the correct folders are returned for exact matches
for fc_dir in fc_dirs:
self.assertListEqual([fc_dir],
IlluminaRun.get_flowcell(subdir,os.path.basename(fc_dir)),
"Did not return the correct folder for exact match")
# Assert that an empty match returns all folders
self.assertListEqual(sorted(fc_dirs),
sorted(IlluminaRun.get_flowcell(subdir)),
"Did not return the correct folders for empty matches")
# Assert that a partial match is resolved to the correct folder
self.assertListEqual([fc_dirs[-1]],
IlluminaRun.get_flowcell(subdir,"{}_fc_dir".format(str(len(fc_dirs)-1))),
"Did not return the correct folder for partial match")
# Assert that an ambiguous match returns the matching folders
self.assertListEqual(sorted(fc_dirs),
sorted(IlluminaRun.get_flowcell(subdir,"_fc_dir")),
"Did not return the correct folders for ambiguous matches")
# Assert that the correct folder is returned for an exact match that matches ambiguously when allowing wildcards
ambig_dir = os.path.join(subdir,"_fc_dir")
utils.safe_makedir(ambig_dir)
self.assertListEqual([ambig_dir],
sorted(IlluminaRun.get_flowcell(subdir,os.path.basename(ambig_dir))),
"Did not return the correct folder for specific non-wildcard match")
shutil.rmtree(subdir)
def test_get_samplesheet(self):
"""Locate the samplesheet in a folder
"""
# Work in a separate subdirectory
subdir = os.path.join(self.rootdir,"test_get_samplesheet")
os.mkdir(subdir)
# Create a few random files and folders and assert that they are not returned
suffixes = [".csv","",""]
for n in range(3):
os.mkdir(os.path.join(subdir,''.join(random.choice(string.ascii_uppercase) for x in range(5))))
fh, _ = tempfile.mkstemp(dir=subdir, suffix=suffixes[n])
os.close(fh)
self.assertIsNone(IlluminaRun.get_samplesheet(subdir),
"Getting non-existing samplesheet did not return None")
# Create a SampleSheet.csv and a [FCID].csv file and assert that they are
# returned with a preference for the [FCID].csv file
fcid = td.generate_fc_barcode()
fcdir = os.path.join(subdir,td.generate_run_id(fc_barcode=fcid))
os.mkdir(fcdir)
ss = [os.path.join(fcdir,"SampleSheet.csv"),
os.path.join(fcdir,"{}.csv".format(fcid))]
for s in ss:
utils.touch_file(s)
self.assertEqual(s,IlluminaRun.get_samplesheet(fcdir),
"Did not get existing {}".format(os.path.basename(s)))
shutil.rmtree(subdir)
def test_get_sequence_dir(self):
"""Get the sequence read directory
"""
self.assertEqual(sorted(self.exp_seqdir), sorted(self.run.get_sequence_dir()),
"Did not get correct top directory for sequence reads")
def test_get_unmatched_dir(self):
"""Get the unmatched indices read top directory
"""
self.assertEqual(sorted(self.exp_unmatched_directory), sorted(self.run.get_unmatched_dir()),
"Did not get correct top directory for undetermined indices sequence reads")
def test_get_basecall_stats(self):
"""Get the basecall stats directory
"""
self.assertEqual(sorted(self.run.get_basecall_stats()), sorted(self.exp_basecall_stats),
"Did not get correct Basecall_Stats directory")
def test_get_unmatched_reads(self):
"""Get the undetermined indexes reads
"""
# Create some files representing undetermined index reads
lanes = [1,3,5,7]
readfiles = []
for lane in lanes:
fdir = os.path.join(self.exp_unmatched_directory[0],"Sample_lane{:d}".format(lane))
readfiles.append([os.path.join(fdir,"lane{l:d}_Undetermined_L00{l:d}_R{r:d}_*.fastq.gz".format(l=lane, r=read)) for read in [1,2]])
os.makedirs(fdir)
for readfile in readfiles[-1]:
utils.touch_file(readfile)
# Assert that the correct files are returned
self.assertListEqual(sorted(readfiles[-1]),
sorted(self.run.get_unmatched_reads(lanes=[lane])[0]),
"Did not get expected undetermined indexes reads")
class TestIlluminaRun(unittest.TestCase):
def setUp(self):
self.rootdir = tempfile.mkdtemp(prefix="test_illumina_run_")
# Create a fcdir
self.exp_fcid = td.generate_fc_barcode()
self.exp_fcdir = os.path.join(
self.rootdir, td.generate_run_id(fc_barcode=self.exp_fcid))
os.mkdir(self.exp_fcdir)
# Create multiple sequence read directories
self.exp_seqdir = [
os.path.join(self.exp_fcdir, "Unaligned"),
os.path.join(self.exp_fcdir, "Unaligned_L6"),
os.path.join(self.exp_fcdir, "Unaligned_L8")
]
for d in self.exp_seqdir:
os.mkdir(d)
# Create directories for undetermined indices reads
self.exp_unmatched_directory = [
os.path.join(d, "Undetermined_indices")
for d in self.exp_seqdir[:-1]
]
for d in self.exp_unmatched_directory:
os.mkdir(d)
# Create basecall stats directories
self.exp_basecall_stats = [
os.path.join(d, "Basecall_Stats_{}".format(self.exp_fcid))
for d in self.exp_seqdir[1:]
]
for d in self.exp_basecall_stats:
os.mkdir(d)
self.run = IlluminaRun(self.exp_fcdir)
def tearDown(self):
shutil.rmtree(self.rootdir)
def test_map_index_name(self):
"""Map index sequences to names
"""
# Some test cases
from scilifelab.illumina.index_definitions import BASIC_LOOKUP
random_keys = [
BASIC_LOOKUP.keys()[random.randint(0,
len(BASIC_LOOKUP.keys()) - 1)]
for n in xrange(25)
]
for name in random_keys:
self.assertIn(name, map_index_name(BASIC_LOOKUP[name], 0),
"Exact mapping did not return expected index name")
def test_get_flowcell(self):
"""Get flowcell from analysis directory
"""
# Work in a separate subdirectory
subdir = os.path.join(self.rootdir, "test_get_flowcell")
os.mkdir(subdir)
# Create some folders
fc_dirs = []
for i in range(3):
fc_dirs.append(
tempfile.mkdtemp(suffix="{}_fc_dir".format(i), dir=subdir))
# Assert nothing is returned for non-existing flowcell
self.assertListEqual(
IlluminaRun.get_flowcell(subdir, 'flowcell_id'), [],
"Nothing should be returned for a non-existing flowcell id")
# Assert that the correct folders are returned for exact matches
for fc_dir in fc_dirs:
self.assertListEqual(
[fc_dir],
IlluminaRun.get_flowcell(subdir, os.path.basename(fc_dir)),
"Did not return the correct folder for exact match")
# Assert that an empty match returns all folders
self.assertListEqual(
sorted(fc_dirs), sorted(IlluminaRun.get_flowcell(subdir)),
"Did not return the correct folders for empty matches")
# Assert that a partial match is resolved to the correct folder
self.assertListEqual(
[fc_dirs[-1]],
IlluminaRun.get_flowcell(subdir, "{}_fc_dir".format(
str(len(fc_dirs) - 1))),
"Did not return the correct folder for partial match")
# Assert that an ambiguous match returns the matching folders
self.assertListEqual(
sorted(fc_dirs),
sorted(IlluminaRun.get_flowcell(subdir, "_fc_dir")),
"Did not return the correct folders for ambiguous matches")
# Assert that the correct folder is returned for an exact match that matches ambiguously when allowing wildcards
ambig_dir = os.path.join(subdir, "_fc_dir")
utils.safe_makedir(ambig_dir)
self.assertListEqual(
[ambig_dir],
sorted(
IlluminaRun.get_flowcell(subdir, os.path.basename(ambig_dir))),
"Did not return the correct folder for specific non-wildcard match"
)
shutil.rmtree(subdir)
def test_get_samplesheet(self):
"""Locate the samplesheet in a folder
"""
# Work in a separate subdirectory
subdir = os.path.join(self.rootdir, "test_get_samplesheet")
os.mkdir(subdir)
# Create a few random files and folders and assert that they are not returned
suffixes = [".csv", "", ""]
for n in range(3):
os.mkdir(
os.path.join(
subdir, ''.join(
random.choice(string.ascii_uppercase)
for x in range(5))))
fh, _ = tempfile.mkstemp(dir=subdir, suffix=suffixes[n])
os.close(fh)
self.assertIsNone(
IlluminaRun.get_samplesheet(subdir),
"Getting non-existing samplesheet did not return None")
# Create a SampleSheet.csv and a [FCID].csv file and assert that they are
# returned with a preference for the [FCID].csv file
fcid = td.generate_fc_barcode()
fcdir = os.path.join(subdir, td.generate_run_id(fc_barcode=fcid))
os.mkdir(fcdir)
ss = [
os.path.join(fcdir, "SampleSheet.csv"),
os.path.join(fcdir, "{}.csv".format(fcid))
]
for s in ss:
utils.touch_file(s)
self.assertEqual(
s, IlluminaRun.get_samplesheet(fcdir),
"Did not get existing {}".format(os.path.basename(s)))
shutil.rmtree(subdir)
def test_get_sequence_dir(self):
"""Get the sequence read directory
"""
self.assertEqual(
sorted(self.exp_seqdir), sorted(self.run.get_sequence_dir()),
"Did not get correct top directory for sequence reads")
def test_get_unmatched_dir(self):
"""Get the unmatched indices read top directory
"""
self.assertEqual(
sorted(self.exp_unmatched_directory),
sorted(self.run.get_unmatched_dir()),
"Did not get correct top directory for undetermined indices sequence reads"
)
def test_get_basecall_stats(self):
"""Get the basecall stats directory
"""
self.assertEqual(sorted(self.run.get_basecall_stats()),
sorted(self.exp_basecall_stats),
"Did not get correct Basecall_Stats directory")
def test_get_unmatched_reads(self):
"""Get the undetermined indexes reads
"""
# Create some files representing undetermined index reads
lanes = [1, 3, 5, 7]
readfiles = []
for lane in lanes:
fdir = os.path.join(self.exp_unmatched_directory[0],
"Sample_lane{:d}".format(lane))
readfiles.append([
os.path.join(
fdir,
"lane{l:d}_Undetermined_L00{l:d}_R{r:d}_*.fastq.gz".format(
l=lane, r=read)) for read in [1, 2]
])
os.makedirs(fdir)
for readfile in readfiles[-1]:
utils.touch_file(readfile)
# Assert that the correct files are returned
self.assertListEqual(
sorted(readfiles[-1]),
sorted(self.run.get_unmatched_reads(lanes=[lane])[0]),
"Did not get expected undetermined indexes reads")
def status_query(archive_dir, analysis_dir, flowcell, project, brief):
"""Get a status report of the progress of flowcells based on a snapshot of the file system
"""
last_step = 14
status = []
# Process each flowcell in the archive directory
for fcdir in IlluminaRun.get_flowcell(archive_dir,flowcell):
fc_status = {}
fc_status['flowcell'] = os.path.basename(fcdir)
# Locate the samplesheet
samplesheet = IlluminaRun.get_samplesheet(fcdir)
if samplesheet is None:
print("{}***ERROR***: Could not locate samplesheet in flowcell directory. Skipping..")
continue
fc_status['samplesheet'] = samplesheet
# Get a list of the projects in the samplesheet
projects = HiSeqRun.get_project_names(samplesheet)
if len(projects) == 0:
print("\t***WARNING***: No projects matched your filter [{}] for flowcell. Skipping..".format(project))
continue
fc_status['projects'] = []
# Iterate over the projects in the flowcell
for proj in projects:
proj = proj.replace("__",".")
proj_status = {}
proj_status['project'] = proj
pdir = bcbio.get_project_analysis_dir(analysis_dir, proj)
if not pdir:
continue
proj_status['project_dir'] = pdir
proj_status['samples'] = []
proj_status['no_finished_samples'] = 0
samples = HiSeqRun.get_project_sample_ids(samplesheet, proj)
for smpl in samples:
smpl = smpl.replace("__",".")
sample_status = {}
proj_status['samples'].append(sample_status)
sample_status['sample_id'] = smpl
sdir = bcbio.get_sample_analysis_dir(pdir, smpl)
if not sdir:
continue
sample_status['sample_dir'] = sdir
# Match the flowcell we're processing to the sample flowcell directories
sample_fc = [d for d in IlluminaRun.get_flowcell(sdir) if d.split("_")[-1] == fcdir.split("_")[-1]]
if len(sample_fc) == 0:
continue
sample_fc = sample_fc[0]
sample_status['sample_fc_dir'] = sample_fc
fastq_screen = bcbio.get_fastq_screen_folder(sample_fc)
if fastq_screen:
sample_status['fastq_screen'] = [fastq_screen,bcbio.fastq_screen_finished(fastq_screen)]
now = datetime.datetime.now()
pipeline_start_indicator = bcbio.get_pipeline_indicator(sample_fc,[1])
if len(pipeline_start_indicator) == 0:
continue
pipeline_start_indicator = pipeline_start_indicator[0]
most_recent, _ = bcbio.get_most_recent_indicator([pipeline_start_indicator])
sample_status['pipeline_started'] = [pipeline_start_indicator,most_recent]
most_recent, ifile = bcbio.get_most_recent_indicator(bcbio.get_pipeline_indicator(sample_fc))
sample_status['pipeline_progress'] = [ifile,most_recent]
sample_log = bcbio.get_sample_pipeline_log(sample_fc,smpl)
if not sample_log:
continue
st = os.stat(sample_log)
sample_status['pipeline_log'] = [sample_log,datetime.datetime.fromtimestamp(st.st_mtime)]
jobids = slurm.get_slurm_jobid(smpl)
sample_status['slurm_job'] = []
for jobid in jobids:
sample_status['slurm_job'].append([jobid,slurm.get_slurm_jobstatus(jobid)])
most_recent, ifile = bcbio.get_most_recent_indicator(bcbio.get_pipeline_indicator(sample_fc,[last_step]))
if ifile is not None and sample_status.get('fastq_screen',[None,False])[1]:
sample_status['finished'] = True
proj_status['no_finished_samples'] += 1
if proj_status['no_finished_samples'] == len(samples):
proj_status['finished'] = True
fc_status['projects'].append(proj_status)
status.append(fc_status)
print_status(status,brief)