def launch_bedcoverage_hist(work_dir,
bed,
bam,
chr_lengths_fpath,
bedcov_output_fpath=None,
bedtools='bedtools'):
if not bedcov_output_fpath:
bedcov_output_fpath = join(
work_dir,
splitext_plus(basename(bed))[0] + '__' +
splitext_plus(basename(bam))[0] + '_bedcov_output.txt')
if bam.endswith('bam'):
bam = bam_to_bed_nocnf(bam, bedtools)
verify_file(bam,
is_critical=True,
description='BAM to BED conversion result')
v = bedtools_version(bedtools)
if v and v >= 24:
cmdline = '{bedtools} coverage -sorted -g {chr_lengths_fpath} -a {bed} -b {bam} -hist'.format(
**locals())
else:
cmdline = '{bedtools} coverage -a {bam} -b {bed} -hist'.format(
**locals())
cmdline += ' > ' + bedcov_output_fpath
info(cmdline)
os.system(cmdline)
res = verify_file(bedcov_output_fpath)
if res:
info('Done, saved to ' + bedcov_output_fpath)
else:
err('Error, result is non-existent or empty')
def set_up_out_dirs(self, fastq_dirpath, fastqc_dirpath,
downsample_targqc_dirpath):
self.fastq_dirpath = fastq_dirpath
self.fastqc_dirpath = fastqc_dirpath
self.downsample_targqc_dirpath = downsample_targqc_dirpath
self.l_fpath = join(fastq_dirpath, self.name + '_R1.fastq.gz')
self.r_fpath = join(fastq_dirpath, self.name + '_R2.fastq.gz')
self.sample_fastqc_dirpath = join(fastqc_dirpath,
self.name + '.fq_fastqc')
self.fastqc_html_fpath = join(fastqc_dirpath,
self.name + '.fq_fastqc.html')
self.l_fastqc_base_name = splitext_plus(basename(self.l_fpath))[0]
self.r_fastqc_base_name = splitext_plus(basename(self.r_fpath))[0]
# self.l_fastqc_html_fpath = None # join(ds.fastqc_dirpath, + '_fastqc.html')
# self.r_fastqc_html_fpath = None # join(ds.fastqc_dirpath, splitext_plus(self.r_fpath)[0] + '_fastqc.html')
if not isfile(self.fastqc_html_fpath):
self.fastqc_html_fpath = join(self.sample_fastqc_dirpath,
'fastqc_report.html')
self.targqc_sample = TargQC_Sample(
self.name, join(downsample_targqc_dirpath, self.name))
self.targetcov_html_fpath = self.targqc_sample.targetcov_html_fpath
self.ngscat_html_fpath = self.targqc_sample.ngscat_html_fpath
self.qualimap_html_fpath = self.targqc_sample.qualimap_html_fpath
def intersect_bed(cnf, bed1, bed2):
bed1_fname, _ = splitext_plus(basename(bed1))
bed2_fname, _ = splitext_plus(basename(bed2))
output_fpath = join(cnf['work_dir'],
bed1_fname + '__' + bed2_fname + '.bed')
bedtools = get_system_path(cnf, 'bedtools')
cmdline = '{bedtools} intersect -u -a {bed1} -b {bed2}'.format(**locals())
call(cnf, cmdline, output_fpath, verify_output_not_empty=False)
return output_fpath
def _intersect_with_tricky_regions(cnf, selected_bed_fpath, sample):
info()
info('Detecting problematic regions for ' + sample)
bed_filenames = [fn + '.bed.gz' for fn in tricky_regions_fnames_d.keys()]
merged_bed_fpaths = [
join(cnf.genome.tricky_regions, 'merged', bed_filename)
for bed_filename in bed_filenames
]
info('Intersecting BED ' + selected_bed_fpath +
' using BED files with tricky regions')
intersection_fpath = join(
cnf.work_dir,
splitext_plus(basename(selected_bed_fpath))[0] +
'_tricky_vcf_bed.intersect')
if not cnf.reuse_intermediate or not verify_file(
intersection_fpath, silent=True, is_critical=False):
bedtools = get_system_path(cnf, 'bedtools')
cmdline = bedtools + ' intersect -header -a ' + selected_bed_fpath + ' -b ' + ' '.join(
merged_bed_fpaths) + ' -wo -filenames'
call(cnf,
cmdline,
output_fpath=intersection_fpath,
exit_on_error=False)
return intersection_fpath
def markdup_bam(cnf, in_bam_fpath, bammarkduplicates=None):
"""Perform non-stream based deduplication of BAM input files using biobambam.
"""
if not bammarkduplicates:
bammarkduplicates = get_system_path(cnf, 'bammarkduplicates')
if not bammarkduplicates:
warn('No biobambam bammarkduplicates, can\'t mark duplicates.')
return None
out_bam_fpath = add_suffix(in_bam_fpath, 'markdup')
tmp_fpath = join(cnf.work_dir,
splitext_plus(basename(in_bam_fpath))[0] + '_markdup')
safe_mkdir(dirname(tmp_fpath))
cmdline = (
'{bammarkduplicates} tmpfile={tmp_fpath} I={in_bam_fpath} O={out_bam_fpath}'
).format(**locals())
res = call(cnf,
cmdline,
output_fpath=out_bam_fpath,
stdout_to_outputfile=False,
exit_on_error=False)
if res:
return out_bam_fpath
else:
return None
def _tracks(cnf, track_fpath, input_fpath):
if not verify_file(track_fpath):
return None
field_name = splitext_plus(basename(track_fpath))[0]
step_greetings('Intersecting with ' + field_name)
output_fpath = intermediate_fname(cnf, input_fpath, field_name)
if output_fpath.endswith('.gz'):
output_fpath = output_fpath[:-3]
if cnf.reuse_intermediate and verify_vcf(output_fpath):
info('VCF ' + output_fpath + ' exists, reusing...')
return output_fpath
toolpath = get_system_path(cnf, 'vcfannotate')
if not toolpath:
err('WARNING: Skipping annotation with tracks: vcfannotate '
'executable not found, you probably need to specify path in system_config, or '
'run load bcbio: . /group/ngs/bin/bcbio-prod.sh"')
return None
# self.all_fields.append(field_name)
cmdline = '{toolpath} -b {track_fpath} -k {field_name} {input_fpath}'.format(
**locals())
assert input_fpath
output_fpath = call_subprocess(cnf,
cmdline,
input_fpath,
output_fpath,
stdout_to_outputfile=True,
overwrite=True)
if not verify_vcf(output_fpath):
err('Error: tracks resulted ' + str(output_fpath) + ' for ' +
track_fpath)
return output_fpath
# Set TRUE or FALSE for tracks
def proc_line(line, i):
if field_name in line:
if not line.startswith('#'):
fields = line.split('\t')
info_line = fields[7]
info_pairs = [attr.split('=') for attr in info_line.split(';')]
info_pairs = [[pair[0], ('TRUE' if pair[1] else 'FALSE')] if
pair[0] == field_name and len(pair) > 1 else pair
for pair in info_pairs]
info_line = ';'.join(
'='.join(pair) if len(pair) == 2 else pair[0]
for pair in info_pairs)
fields = fields[:7] + [info_line] + fields[8:]
return '\t'.join(fields)
return line
assert output_fpath
output_fpath = iterate_file(cnf, output_fpath, proc_line, suffix='trk')
return verify_vcf(output_fpath, is_critical=True)
def sambamba_depth(cnf,
bed,
bam,
output_fpath=None,
use_grid=False,
depth_thresholds=None,
sample_name=None,
only_depth=False,
silent=False):
sample_name = sample_name or splitext_plus(basename(bam))[0]
if not output_fpath:
output_fpath = join(
cnf.work_dir,
splitext_plus(basename(bed))[0] + '_' + sample_name +
'_sambamba_depth.txt')
if cnf.reuse_intermediate and verify_file(output_fpath, silent=True):
info(output_fpath + ' exists, reusing.')
if use_grid:
return None
else:
return output_fpath
sambamba = get_system_path(cnf,
join(get_ext_tools_dirname(), 'sambamba'),
is_critical=True)
thresholds_str = ''
if not only_depth:
depth_thresholds = depth_thresholds or cnf.coverage_reports.depth_thresholds
thresholds_str = '-T ' + ' -T'.join([str(d) for d in depth_thresholds])
cmdline = 'depth region -F "not duplicate and not failed_quality_control" -L {bed} {thresholds_str} {bam}'.format(
**locals())
return call_sambamba(cnf,
cmdline,
output_fpath=output_fpath,
bam_fpath=bam,
sambamba=sambamba,
use_grid=use_grid,
command_name='depth_' +
splitext_plus(basename(bed))[0],
sample_name=sample_name,
silent=silent)
def create_jbrowse_symlink(genome, project_name, sample, file_fpath):
jbrowse_data_path, _, _ = set_folders(genome)
jbrowse_dirpath = join(jbrowse_data_path, 'tracks')
jbrowse_project_dirpath = join(jbrowse_dirpath, project_name)
base, ext = splitext_plus(file_fpath)
if ext in ['.tbi', '.bai']:
base, ext2 = splitext_plus(base)
ext = ext2 + ext
sym_link = join(jbrowse_project_dirpath, sample + ext)
if not verify_dir(jbrowse_project_dirpath):
safe_mkdir(jbrowse_project_dirpath)
if isfile(file_fpath) and not isfile(sym_link):
try:
os.symlink(file_fpath, sym_link)
except OSError:
warn(traceback.format_exc())
if isfile(sym_link):
change_permissions(sym_link)
return sym_link
def bam_to_bed_nocnf(bam_fpath, bedtools='bedtools', gzip='gzip'):
info(
'Converting the BAM to BED to save some memory.'
) # from here: http://davetang.org/muse/2015/08/05/creating-a-coverage-plot-using-bedtools-and-r/
bam_bed_fpath = splitext_plus(bam_fpath)[0] + '.bed.gz'
cmdline = '{bedtools} bamtobed -i {bam_fpath} | {gzip} > {bam_bed_fpath}'.format(
**locals())
info(cmdline)
os.system(cmdline)
bam_bed_fpath = verify_file(bam_bed_fpath)
if bam_bed_fpath:
info('Done, saved to ' + bam_bed_fpath)
else:
err('Error, result is non-existent or empty')
return bam_bed_fpath
def bam_to_bed(cnf, bam_fpath, to_gzip=True):
info(
'Converting the BAM to BED to save some memory.'
) # from here: http://davetang.org/muse/2015/08/05/creating-a-coverage-plot-using-bedtools-and-r/
bam_bed_fpath = splitext_plus(bam_fpath)[0] + ('.bed.gz'
if to_gzip else '.bed')
bedtools = get_system_path(cnf, 'bedtools')
gzip = get_system_path(cnf, 'gzip')
cmdline = '{bedtools} bamtobed -i {bam_fpath}'.format(**locals())
cmdline += ' | {gzip}'.format(**locals()) if to_gzip else ''
call(cnf,
cmdline,
output_fpath=bam_bed_fpath,
verify_output_not_empty=False)
return bam_bed_fpath
def markdup_sam(cnf, in_sam_fpath, samblaster=None):
"""Perform non-stream based deduplication of SAM input files using samblaster.
"""
if not samblaster:
samblaster = get_system_path(cnf, 'samblaster')
if not samblaster:
warn('No samblaster, can\'t mark duplicates.')
return None
out_sam_fpath = add_suffix(in_sam_fpath, 'markdup')
tmp_fpath = join(cnf.work_dir,
splitext_plus(basename(in_sam_fpath))[0] + '_markdup')
safe_mkdir(dirname(tmp_fpath))
cmdline = '{samblaster} -i {in_sam_fpath} -o {out_sam_fpath}'.format(
**locals())
res = call(cnf,
cmdline,
output_fpath=out_sam_fpath,
stdout_to_outputfile=False,
exit_on_error=False)
if res:
return out_sam_fpath
else:
return None
def read_samples_info_and_split(common_cnf, options, inputs):
#TODO: _set_up_dirs(cnf) for each sample
info('')
info('Processing input details...')
details = None
for key in inputs:
if options.get(key):
common_cnf[key] = adjust_path(options[key])
info('Using ' + common_cnf[key])
details = [common_cnf]
if not details:
details = common_cnf.get('details')
if not details:
critical('Please, provide input ' + ', '.join(inputs) +
' in command line or in run info yaml config.')
all_samples = OrderedDict()
for one_item_cnf in details:
if 'vcf' not in one_item_cnf:
critical('ERROR: A section in details does not contain field "var".')
one_item_cnf['vcf'] = adjust_path(one_item_cnf['vcf'])
verify_file(one_item_cnf['vcf'], 'Input file', is_critical=True)
join_parent_conf(one_item_cnf, common_cnf)
work_vcf = join(one_item_cnf['work_dir'], basename(one_item_cnf['vcf']))
check_file_changed(one_item_cnf, one_item_cnf['vcf'], work_vcf)
if not one_item_cnf.get('reuse_intermediate'):
with open_gzipsafe(one_item_cnf['vcf']) as inp, open_gzipsafe(work_vcf, 'w') as out:
out.write(inp.read())
one_item_cnf['vcf'] = work_vcf
vcf_header_samples = read_sample_names_from_vcf(one_item_cnf['vcf'])
# MULTIPLE SAMPELS
if ('samples' in one_item_cnf or one_item_cnf.get('split_samples')) and len(vcf_header_samples) == 0:
sample_cnfs = _verify_sample_info(one_item_cnf, vcf_header_samples)
for header_sample_name in vcf_header_samples:
if header_sample_name not in sample_cnfs:
sample_cnfs[header_sample_name] = one_item_cnf.copy()
if header_sample_name in all_samples:
critical('ERROR: duplicated sample name: ' + header_sample_name)
cnf = all_samples[header_sample_name] = sample_cnfs[header_sample_name]
cnf['name'] = header_sample_name
if cnf.get('keep_intermediate'):
cnf['log'] = join(cnf['work_dir'], cnf['name'] + '.log')
# cnf['vcf'] = extract_sample(cnf, one_item_cnf['vcf'], cnf['name'])
info()
# SINGLE SAMPLE
else:
cnf = one_item_cnf
if 'bam' in cnf:
cnf['bam'] = adjust_path(cnf['bam'])
verify_bam(cnf['bam'], is_critical=True)
cnf['name'] = splitext_plus(basename(cnf['vcf']))[0]
if cnf.get('keep_intermediate'):
cnf['log'] = join(cnf['work_dir'], cnf['name'] + '.log')
cnf['vcf'] = work_vcf
all_samples[cnf['name']] = cnf
if not all_samples:
info('No samples.')
else:
info('Using samples: ' + ', '.join(all_samples) + '.')
return all_samples
def _extract_fields(cnf, vcf_fpath, samplename, main_sample_index=0):
fname, _ = splitext_plus(basename(vcf_fpath))
tsv_fpath = join(cnf.work_dir, fname + '.tsv')
if cnf.get('reuse_intermediate'):
if file_exists(tsv_fpath):
info(tsv_fpath + ' exists, reusing')
return tsv_fpath
manual_tsv_fields = cnf.annotation['tsv_fields']
if not manual_tsv_fields:
return None
all_fields = []
basic_fields = []
info_fields = []
eff_fields = []
gt_fields = []
tumor_gt = 'GEN[' + str(main_sample_index) + '].'
normal_gt = 'GEN[' + str(1 - main_sample_index) + '].'
lines = []
with open(vcf_fpath) as inp:
reader = vcf.Reader(inp)
info('TSV saver: Building field list')
for f in [rec.keys()[0] for rec in manual_tsv_fields]:
if f.startswith('GEN'):
_f = f.split('.')[1]
if len(reader.samples) > 0:
if _f in reader.formats:
gt_fields.append(_f)
all_fields.append(f.replace('GEN[*].', tumor_gt))
if len(reader.samples) > 1:
all_fields.append(f.replace('GEN[*].', normal_gt))
else:
warn('TSV Saver: Warning: ' + f + ' is not in VCF header FORMAT records')
elif f in ['CHROM', 'POS', 'REF', 'ALT', 'ID', 'FILTER', 'QUAL']:
all_fields.append(f)
basic_fields.append(f)
elif any(f.startswith(af) and af in reader.infos for af in ['EFF', 'ANN']):
all_fields.append(f)
eff_fields.append(f)
else:
if f in reader.infos:
info_fields.append(f)
all_fields.append(f)
elif f == 'SAMPLE':
all_fields.append(f)
else:
warn('TSV Saver: Warning: ' + f + ' is not in VCF header INFO records')
info('TSV saver: Iterating over records...')
d = OrderedDict()
for rec in reader:
for f in basic_fields:
d[f] = rec.__dict__[f]
for f in info_fields:
d[f] = rec.INFO[f] if f in rec.INFO else ''
if 'SAMPLE' not in d:
d['SAMPLE'] = samplename
if eff_fields:
eff = rec.INFO.get(eff_fields[0][:3])
if not eff:
for f in eff_fields:
d[f] = ''
else:
eff_fs = eff[0].split('|')
eff_d = dict()
for val, header in zip(eff_fs, ['ALLELE', 'EFFECT', 'IMPACT', 'GENE', 'GENEID', 'FEATURE', 'FEATUREID', 'BIOTYPE', 'RANK', 'HGVS_C', 'HGVS_P', 'CDNA_POSLEN', 'CDS_POSLEN', 'AA_POSLEN', 'DISTANCE', 'LOG']):
if 'POSLEN' in header:
eff_d[header.split('_')[0] + '_POS'] = val.split('/')[0] if val else ''
eff_d[header.split('_')[0] + '_LEN'] = val.split('/')[1] if val else ''
else:
eff_d[header] = val
#ANN=GA |3_prime_UTR_variant|MODIFIER|RPL22|RPL22|transcript|NM_000983.3|Coding|4/4|c.*173dupT|||||173|;
#Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'
for f in eff_fields:
d[f] = eff_d[f.split('.')[1]]
if rec.FORMAT:
for _f in gt_fields:
if _f in rec.FORMAT:
d[tumor_gt + _f] = rec.samples[main_sample_index][_f]
if len(rec.samples) > 1 - main_sample_index:
d[normal_gt + _f] = rec.samples[1 - main_sample_index][_f]
else:
d[normal_gt + _f] = ''
else:
d[tumor_gt + _f] = ''
d[normal_gt + _f] = ''
fs = []
for f in all_fields:
v = d[f]
fs.append(v if v != '.' else '')
lines.append(fs)
info('TSV saver: Adding GEN[*] fields both for sample and for matched normal...')
field_map = dict()
for rec in manual_tsv_fields:
k = rec.keys()[0]
v = rec.values()[0]
if k.startswith('GEN[*].'):
_f = k.split('.')[1]
field_map[tumor_gt + _f] = v
field_map[normal_gt + _f] = 'Matched_' + v
else:
field_map[k] = v
info('TSV saver: Writing TSV to ' + tsv_fpath)
with file_transaction(cnf.work_dir, tsv_fpath) as tx:
with open(tx, 'w') as out:
out.write('\t'.join(field_map[f] for f in all_fields) + '\n')
for fs in lines:
new_fs = []
for f in fs:
if isinstance(f, list):
new_fs.append(','.join(map(str, f)))
elif f is None:
new_fs.append('')
else:
new_fs.append(str(f))
out.write('\t'.join(new_fs) + '\n')
info('TSV saver: saved ' + tsv_fpath)
return tsv_fpath
def read_samples(args, caller_name=None):
vcf_fpath_by_sample = OrderedDict()
bad_vcf_fpaths = []
info('Reading samples...')
if len(args) == 1:
first_fpath = args[0]
if not first_fpath.endswith('.vcf') and not first_fpath.endswith(
'.vcf.gz'): # TODO: check ##fileformat=VCF ?
info(
'First argument file name does not look like VCF, assuming TSV with files names'
)
with open(first_fpath) as f:
for i, l in enumerate(f):
fs = l.strip().split('\t')
if len(fs) != 2:
critical('Line ' + str(i) + ' has only ' +
str(len(fs)) +
' fields. Expecting 2 (sample and vcf_fpath)')
sn, vcf_fpath = fs
if not verify_file(vcf_fpath):
bad_vcf_fpaths.append(vcf_fpath)
vcf_fpath_by_sample[sn] = adjust_path(vcf_fpath)
if bad_vcf_fpaths:
critical('VCF files cannot be found, empty or not VCFs:' +
', '.join(bad_vcf_fpaths))
info('Done reading ' + str(len(vcf_fpath_by_sample)) + ' samples')
return vcf_fpath_by_sample
for arg in args or [os.getcwd()]:
vcf_fpath = verify_vcf(arg.split(',')[0])
if not verify_file(vcf_fpath):
bad_vcf_fpaths.append(vcf_fpath)
if len(arg.split(',')) > 1:
sn = arg.split(',')[1]
else:
sn = basename(splitext_plus(vcf_fpath)[0])
if caller_name and sn.endswith('-' + caller_name):
sn = sn[:-len(caller_name) - 1]
info(' ' + sn)
if sn in vcf_fpath_by_sample:
if vcf_fpath_by_sample[sn] != vcf_fpath:
warn('Duplicated record ' + sn +
', VCF file is different (existing: ' +
vcf_fpath_by_sample[sn] + ', new: ' + vcf_fpath + ')')
else:
warn('Duplicated record ' + sn + ', VCF file is the same: ' +
vcf_fpath)
else:
vcf_fpath_by_sample[sn] = vcf_fpath
if bad_vcf_fpaths:
critical('VCF files cannot be found, empty or not VCFs:' +
', '.join(bad_vcf_fpaths))
info('Done reading ' + str(len(vcf_fpath_by_sample)) + ' samples')
# TODO: read sample names from VCF
# def get_main_sample(self, main_sample_index=None):
# if len(self._sample_indexes) == 0:
# return None
# if main_sample_index is not None:
# return self.samples[main_sample_index]
# try:
# sample_index = [sname.lower() for sname in self._sample_indexes] \
# .index(self.sample_name_from_file.lower())
# except ValueError:
# return self.samples[0]
# else:
# return self.samples[sample_index]
return vcf_fpath_by_sample
def make_fastqc_reports(cnf, fastq_fpaths, output_dir):
# if isdir(fastqc_dirpath):
# if isdir(fastqc_dirpath + '.bak'):
# try:
# shutil.rmtree(fastqc_dirpath + '.bak')
# except OSError:
# pass
# if not isdir(fastqc_dirpath + '.bak'):
# os.rename(fastqc_dirpath, fastqc_dirpath + '.bak')
# if isdir(fastqc_dirpath):
# err('Could not run and combine fastqc because it already exists and could not be moved to fastqc.bak')
# return None
fastqc = get_system_path(cnf, 'fastqc')
if not fastqc:
err('FastQC is not found, cannot make reports')
return None
else:
safe_mkdir(output_dir)
fqc_samples = []
fastqc_jobs = []
for fastq_fpath in fastq_fpaths:
s = FQC_Sample(name=splitext_plus(basename(fastq_fpath))[0],
fastq_fpath=fastq_fpath)
fqc_samples.extend([s])
info('Added sample ' + s.name)
for fqc_s in fqc_samples:
if cnf.reuse_intermediate and verify_file(fqc_s.fastqc_html_fpath,
silent=True):
info(fqc_s.fastqc_html_fpath + ' exists, reusing')
else:
fastqc_jobs.append(
run_fastqc(cnf, fqc_s.fastq_fpath, fqc_s.name, output_dir))
info()
wait_for_jobs(cnf, fastqc_jobs)
fastqc_jobs = []
# while True:
for fqc_s in fqc_samples:
fqc_s.fastqc_html_fpath = find_fastqc_html(output_dir, fqc_s.name)
not_done_fqc = [
fqc_s for fqc_s in fqc_samples
if not verify_file(fqc_s.fastqc_html_fpath,
description='Not found FastQC html for ' +
fqc_s.name)
]
# if not not_done_fqc:
# info('')
# info('Every FastQC job is done, moving on.')
# info('-' * 70)
# break
# else:
# info('')
# info('Some FastQC jobs are not done (' + ', '.join(f.name for f in not_done_fqc) + '). Retrying them.')
# info('')
# for fqc_s in not_done_fqc:
# fastqc_jobs.append(run_fastqc(cnf, fqc_s.fastq_fpath, fqc_s.name, output_dir))
# wait_for_jobs(cnf, fastqc_jobs)
for fqc_s in fqc_samples:
sample_fastqc_dirpath = join(output_dir, fqc_s.name + '_fastqc')
if isfile(sample_fastqc_dirpath + '.zip'):
try:
os.remove(sample_fastqc_dirpath + '.zip')
except OSError:
pass
comb_fastqc_fpath = join(output_dir, 'fastqc.html')
write_fastqc_combo_report(cnf, comb_fastqc_fpath, fqc_samples)
verify_file(comb_fastqc_fpath, is_critical=True)
info('Combined FastQC saved to ' + comb_fastqc_fpath)
return comb_fastqc_fpath
