def run_main(config, config_file, fc_dir, run_info_yaml):
work_dir = os.getcwd()
fc_name, fc_date = get_flowcell_info(fc_dir)
if run_info_yaml and os.path.exists(run_info_yaml):
log.info("Found YAML samplesheet, using %s instead of Galaxy API" % run_info_yaml)
with open(run_info_yaml) as in_handle:
run_details = yaml.load(in_handle)
run_info = dict(details=run_details, run_id="")
else:
log.info("Fetching run details from Galaxy instance")
galaxy_api = GalaxyApiAccess(config['galaxy_url'], config['galaxy_api_key'])
run_info = galaxy_api.run_details(fc_name, fc_date)
fastq_dir = get_fastq_dir(fc_dir)
run_items = _add_multiplex_across_lanes(run_info["details"], fastq_dir, fc_name)
align_dir = os.path.join(work_dir, "alignments")
# process each flowcell lane
with utils.cpmap(config["algorithm"]["num_cores"]) as cpmap:
for _ in cpmap(process_lane,
((i, fastq_dir, fc_name, fc_date, align_dir, config, config_file)
for i in run_items)):
pass
# process samples, potentially multiplexed across multiple lanes
sample_files, sample_fastq, sample_info = organize_samples(align_dir,
fastq_dir, work_dir, fc_name, fc_date, run_items)
with utils.cpmap(config["algorithm"]["num_cores"]) as cpmap:
for _ in cpmap(process_sample, ((name, sample_fastq[name], sample_info[name],
bam_files, work_dir, config, config_file)
for name, bam_files in sample_files)):
pass
write_metrics(run_info, work_dir, fc_dir, fc_name, fc_date, fastq_dir)
def _generate_fastq(fc_dir, config, compress_fastq):
"""Generate fastq files for the current flowcell.
"""
fc_name, fc_date = get_flowcell_info(fc_dir)
short_fc_name = "%s_%s" % (fc_date, fc_name)
fastq_dir = get_fastq_dir(fc_dir)
basecall_dir = os.path.split(fastq_dir)[0]
postprocess_dir = config.get("postprocess_dir", "")
if postprocess_dir:
fastq_dir = os.path.join(postprocess_dir, os.path.basename(fc_dir), "fastq")
if not fastq_dir == fc_dir:# and not os.path.exists(fastq_dir):
with utils.chdir(basecall_dir):
lanes = sorted(list(set([f.split("_")[1] for f in
glob.glob("*qseq.txt")])))
cl = ["solexa_qseq_to_fastq.py", short_fc_name,
",".join(lanes)]
if postprocess_dir:
cl += ["-o", fastq_dir]
if compress_fastq:
cl += ["--gzip"]
logger2.debug("Converting qseq to fastq on all lanes.")
subprocess.check_call(cl)
return fastq_dir
def run_main(config, config_file, fc_dir, work_dir, run_info_yaml):
align_dir = os.path.join(work_dir, "alignments")
run_module = "bcbio.distributed"
fc_name, fc_date, run_info = get_run_info(fc_dir, config, run_info_yaml)
fastq_dir, galaxy_dir, config_dir = _get_full_paths(
get_fastq_dir(fc_dir), config, config_file)
config_file = os.path.join(config_dir, os.path.basename(config_file))
dirs = {
"fastq": fastq_dir,
"galaxy": galaxy_dir,
"align": align_dir,
"work": work_dir,
"flowcell": fc_dir,
"config": config_dir
}
run_parallel = parallel_runner(run_module, dirs, config, config_file)
# process each flowcell lane
run_items = add_multiplex_across_lanes(run_info["details"], dirs["fastq"],
fc_name)
lanes = ((info, fc_name, fc_date, dirs, config) for info in run_items)
lane_items = run_parallel("process_lane", lanes)
align_items = run_parallel("process_alignment", lane_items)
# process samples, potentially multiplexed across multiple lanes
samples = organize_samples(align_items, dirs, config_file)
samples = run_parallel("merge_sample", samples)
samples = run_parallel("recalibrate_sample", samples)
samples = parallel_realign_sample(samples, run_parallel)
samples = parallel_variantcall(samples, run_parallel)
samples = run_parallel("process_sample", samples)
samples = run_parallel("generate_bigwig", samples,
{"programs": ["ucsc_bigwig"]})
write_project_summary(samples)
write_metrics(run_info, fc_name, fc_date, dirs)
def run_main(config, config_file, work_dir, parallel,
fc_dir=None, run_info_yaml=None):
"""
Run toplevel analysis, processing a set of input files.
config_file -- Main YAML configuration file with system parameters
fc_dir -- Directory of fastq files to process
run_info_yaml -- YAML configuration file specifying inputs to process
"""
setup_logging(config)
fc_name, fc_date, run_info = get_run_info(fc_dir, config, run_info_yaml)
fastq_dir, galaxy_dir, config_dir = _get_full_paths(get_fastq_dir(fc_dir)
if fc_dir else None,
config, config_file)
config_file = os.path.join(config_dir, os.path.basename(config_file))
dirs = {"fastq": fastq_dir, "galaxy": galaxy_dir,
"work": work_dir, "flowcell": fc_dir, "config": config_dir}
run_parallel = parallel_runner(parallel, dirs, config, config_file)
# process each flowcell lane
run_items = add_multiplex_across_lanes(run_info["details"],
dirs["fastq"], fc_name)
lanes = ((info, fc_name, fc_date, dirs, config) for info in run_items)
lane_items = run_parallel("process_lane", lanes)
pipelines = _pair_lanes_with_pipelines(lane_items)
for pipeline, pipeline_items in pipelines.items():
for xs in pipeline.run(config, config_file, run_parallel, dirs, pipeline_items):
assert len(xs) == 1
upload.from_sample(xs[0])
write_metrics(run_info, fc_name, fc_date, dirs)
def _generate_fastq(fc_dir, config, compress_fastq):
"""Generate fastq files for the current flowcell.
"""
fc_name, fc_date = get_flowcell_info(fc_dir)
short_fc_name = "%s_%s" % (fc_date, fc_name)
fastq_dir = get_fastq_dir(fc_dir)
basecall_dir = os.path.split(fastq_dir)[0]
postprocess_dir = config.get("postprocess_dir", "")
if postprocess_dir:
fastq_dir = os.path.join(postprocess_dir, os.path.basename(fc_dir), "fastq")
if not fastq_dir == fc_dir: # and not os.path.exists(fastq_dir):
with utils.chdir(basecall_dir):
lanes = sorted(list(set([f.split("_")[1] for f in
glob.glob("*qseq.txt")])))
cl = ["solexa_qseq_to_fastq.py", short_fc_name,
",".join(lanes)]
if postprocess_dir:
cl += ["-o", fastq_dir]
if compress_fastq:
cl += ["--gzip"]
logger2.debug("Converting qseq to fastq on all lanes.")
subprocess.check_call(cl)
return fastq_dir
def run_main(config, config_file, fc_dir, run_info_yaml):
work_dir = os.getcwd()
align_dir = os.path.join(work_dir, "alignments")
fc_name, fc_date = get_flowcell_info(fc_dir)
run_info = _get_run_info(fc_name, fc_date, config, run_info_yaml)
fastq_dir, galaxy_dir, config_dir = _get_full_paths(get_fastq_dir(fc_dir),
config, config_file)
config_file = os.path.join(config_dir, os.path.basename(config_file))
dirs = {"fastq": fastq_dir, "galaxy": galaxy_dir, "align": align_dir,
"work": work_dir, "flowcell": fc_dir, "config": config_dir}
run_items = add_multiplex_across_lanes(run_info["details"], dirs["fastq"], fc_name)
# process each flowcell lane
lanes = ((info, fc_name, fc_date, dirs, config) for info in run_items)
lane_items = _run_parallel("process_lane", lanes, dirs, config)
_run_parallel("process_alignment", lane_items, dirs, config)
# process samples, potentially multiplexed across multiple lanes
sample_files, sample_fastq, sample_info = \
organize_samples(dirs, fc_name, fc_date, run_items)
samples = ((n, sample_fastq[n], sample_info[n], bam_files, dirs, config, config_file)
for n, bam_files in sample_files)
_run_parallel("process_sample", samples, dirs, config)
write_metrics(run_info, fc_name, fc_date, dirs)
def select_upload_files(base, bc_id, fc_dir, analysis_dir):
"""Select fastq, bam alignment and summary files for upload to Galaxy.
"""
fastq_dir = analysis_dir if bc_id else get_fastq_dir(fc_dir)
for fname in glob.glob(os.path.join(fastq_dir, "%s_*fastq.txt" % base)):
yield (fname, os.path.basename(fname))
for summary_file in glob.glob(
os.path.join(analysis_dir, "%s-*summary.pdf" % base)):
yield (summary_file, _name_with_ext(summary_file, "-summary.pdf"))
for bam_file in glob.glob(
os.path.join(analysis_dir, "%s-*sort-dup.bam" % base)):
yield (bam_file, _name_with_ext(bam_file, ".bam"))
for wig_file in glob.glob(
os.path.join(analysis_dir, "%s-*sort.bigwig" % base)):
yield (wig_file, _name_with_ext(wig_file, "-coverage.bigwig"))
# upload any recalibrated BAM files used for SNP calling
found_recal = False
for bam_file in glob.glob(
os.path.join(analysis_dir,
"%s-*gatkrecal-realign-sort.bam" % base)):
found_recal = True
yield (bam_file, _name_with_ext(bam_file, "-gatkrecal-realign.bam"))
if not found_recal:
for bam_file in glob.glob(
os.path.join(analysis_dir, "%s-*gatkrecal.bam" % base)):
yield (bam_file, _name_with_ext(bam_file, "-gatkrecal.bam"))
# Genotype files produced by SNP calling
for snp_file in glob.glob(
os.path.join(analysis_dir, "%s-*snp-filter.vcf" % base)):
yield (snp_file, _name_with_ext(bam_file, "-snp-filter.vcf"))
# Effect information on SNPs
for snp_file in glob.glob(
os.path.join(analysis_dir, "%s-*snp-filter-effects.tsv" % base)):
yield (snp_file, _name_with_ext(bam_file, "-snp-effects.tsv"))
def run_main(config, config_file, work_dir, parallel,
fc_dir=None, run_info_yaml=None):
"""Run toplevel analysis, processing a set of input files.
config_file -- Main YAML configuration file with system parameters
fc_dir -- Directory of fastq files to process
run_info_yaml -- YAML configuration file specifying inputs to process
"""
setup_logging(config)
align_dir = os.path.join(work_dir, "alignments")
fc_name, fc_date, run_info = get_run_info(fc_dir, config, run_info_yaml)
fastq_dir, galaxy_dir, config_dir = _get_full_paths(get_fastq_dir(fc_dir) if fc_dir else None,
config, config_file)
config_file = os.path.join(config_dir, os.path.basename(config_file))
dirs = {"fastq": fastq_dir, "galaxy": galaxy_dir, "align": align_dir,
"work": work_dir, "flowcell": fc_dir, "config": config_dir}
config = _set_resources(parallel, config)
run_parallel = parallel_runner(parallel, dirs, config, config_file)
## process each flowcell lane
#run_items = add_multiplex_across_lanes(run_info["details"], dirs["fastq"], fc_name)
#lanes = ((info, fc_name, fc_date, dirs, config) for info in run_items)
#lane_items = run_parallel("process_lane", lanes)
logger.info (">>> Parse lane")
lane_items = parse_lane(run_info["details"], fc_name, fc_date, dirs, config)
#for item in lane_items:
#utils.prettyprint_dict(item)
logger.info (">>> Process alignment")
align_items = run_parallel("process_alignment", lane_items)
## process samples, potentially multiplexed across multiple lanes
samples = organize_samples(align_items, dirs, config_file)
logger.info (">>> Merge samples")
samples = run_parallel("merge_sample", samples)
logger.info (">>> Recalibrate samples")
samples = run_parallel("recalibrate_sample", samples)
logger.info (">>> realign sample")
samples = parallel_realign_sample(samples, run_parallel)
logger.info (">>> variantcall")
samples = parallel_variantcall(samples, run_parallel)
logger.info (">>> postprocess_variatns")
samples = run_parallel("postprocess_variants", samples)
logger.info (">>> combine_multiple_calles")
samples = combine_multiple_callers(samples)
logger.info (">>> detect_sv")
samples = run_parallel("detect_sv", samples)
logger.info (">>> combine_calls")
samples = run_parallel("combine_calls", samples)
logger.info (">>> process_sample")
run_parallel("process_sample", samples)
logger.info (">>> Generate bigwig")
run_parallel("generate_bigwig", samples, {"programs": ["ucsc_bigwig"]})
logger.info (">>> Writing project summary")
write_project_summary(samples)
logger.info (">>> Writing metrics")
write_metrics(run_info, fc_name, fc_date, dirs)
logger.info (">>> Done")
def select_upload_files(lane, fc_dir, analysis_dir):
"""Select fastq, bam alignment and summary files for upload to Galaxy.
"""
# fastq, summary and alignment file
for fname in glob.glob(os.path.join(get_fastq_dir(fc_dir),
"%s_*_fastq.txt" % lane)):
yield (fname, os.path.basename(fname))
for summary_file in glob.glob(os.path.join(analysis_dir,
"%s_*-summary.pdf" % lane)):
yield (summary_file, _name_with_ext(summary_file, "-summary.pdf"))
for bam_file in glob.glob(os.path.join(analysis_dir,
"%s_*-sort-dup.bam" % lane)):
yield (bam_file, _name_with_ext(bam_file, ".bam"))
for wig_file in glob.glob(os.path.join(analysis_dir,
"%s_*-sort.bigwig" % lane)):
yield (wig_file, _name_with_ext(wig_file, "-coverage.bigwig"))
# upload any recalibrated BAM files used for SNP calling
found_recal = False
for bam_file in glob.glob(os.path.join(analysis_dir,
"%s_*-gatkrecal-realign-sort.bam" % lane)):
found_recal = True
yield (bam_file, _name_with_ext(bam_file, "-gatkrecal-realign.bam"))
if not found_recal:
for bam_file in glob.glob(os.path.join(analysis_dir,
"%s_*-gatkrecal.bam" % lane)):
yield (bam_file, _name_with_ext(bam_file, "-gatkrecal.bam"))
# Genotype files produced by SNP calling
for snp_file in glob.glob(os.path.join(analysis_dir,
"%s_*-snp-filter.vcf" % lane)):
yield (snp_file, _name_with_ext(bam_file, "-snp-filter.vcf"))
def run_main(config, config_file, fc_dir, work_dir, run_info_yaml):
align_dir = os.path.join(work_dir, "alignments")
run_module = "bcbio.distributed"
fc_name, fc_date, run_info = get_run_info(fc_dir, config, run_info_yaml)
fastq_dir, galaxy_dir, config_dir = _get_full_paths(get_fastq_dir(fc_dir), config, config_file)
config_file = os.path.join(config_dir, os.path.basename(config_file))
dirs = {
"fastq": fastq_dir,
"galaxy": galaxy_dir,
"align": align_dir,
"work": work_dir,
"flowcell": fc_dir,
"config": config_dir,
}
run_parallel = parallel_runner(run_module, dirs, config, config_file)
# process each flowcell lane
run_items = add_multiplex_across_lanes(run_info["details"], dirs["fastq"], fc_name)
lanes = ((info, fc_name, fc_date, dirs, config) for info in run_items)
lane_items = run_parallel("process_lane", lanes)
align_items = run_parallel("process_alignment", lane_items)
# process samples, potentially multiplexed across multiple lanes
samples = organize_samples(align_items, dirs, config_file)
samples = run_parallel("merge_sample", samples)
samples = run_parallel("recalibrate_sample", samples)
samples = parallel_realign_sample(samples, run_parallel)
samples = parallel_variantcall(samples, run_parallel)
samples = run_parallel("detect_sv", samples)
samples = run_parallel("process_sample", samples)
samples = run_parallel("generate_bigwig", samples, {"programs": ["ucsc_bigwig"]})
write_project_summary(samples)
write_metrics(run_info, fc_name, fc_date, dirs)
def _run_toplevel(config, config_file, work_dir, parallel,
fc_dir=None, run_info_yaml=None):
"""
Run toplevel analysis, processing a set of input files.
config_file -- Main YAML configuration file with system parameters
fc_dir -- Directory of fastq files to process
run_info_yaml -- YAML configuration file specifying inputs to process
"""
parallel = log.create_base_logger(config, parallel)
log.setup_local_logging(config, parallel)
fastq_dir, galaxy_dir, config_dir = _get_full_paths(get_fastq_dir(fc_dir)
if fc_dir else None,
config, config_file)
config_file = os.path.join(config_dir, os.path.basename(config_file))
dirs = {"fastq": fastq_dir, "galaxy": galaxy_dir,
"work": work_dir, "flowcell": fc_dir, "config": config_dir}
run_items = run_info.organize(dirs, config, run_info_yaml)
run_parallel = parallel_runner(parallel, dirs, config, config_file)
# process each flowcell lane
lane_items = lane.process_all_lanes(run_items, run_parallel)
pipelines = _pair_lanes_with_pipelines(lane_items)
final = []
with utils.curdir_tmpdir() as tmpdir:
tempfile.tempdir = tmpdir
for pipeline, pipeline_items in pipelines.items():
pipeline_items = _add_provenance(pipeline_items, dirs, run_parallel, parallel, config)
versioncheck.testall(pipeline_items)
for xs in pipeline.run(config, config_file, run_parallel, parallel, dirs, pipeline_items):
if len(xs) == 1:
upload.from_sample(xs[0])
final.append(xs[0])
def main(config_file, fc_dir):
work_dir = os.getcwd()
with open(config_file) as in_handle:
config = yaml.load(in_handle)
galaxy_api = GalaxyApiAccess(config['galaxy_url'], config['galaxy_api_key'])
fc_name, fc_date = get_flowcell_info(fc_dir)
run_info = galaxy_api.run_details(fc_name)
fastq_dir = get_fastq_dir(fc_dir)
#print "Generating fastq files"
#all_lanes = [i['lane'] for i in run_info["details"]]
#short_fc_name = "%s_%s" % (fc_date, fc_name)
#fastq_dir = generate_fastq(fc_dir, short_fc_name, all_lanes)
if config["algorithm"]["num_cores"] > 1:
pool = Pool(config["algorithm"]["num_cores"])
try:
pool.map(_process_wrapper,
((i, fastq_dir, fc_name, fc_date, config, config_file)
for i in run_info["details"]))
except:
pool.terminate()
raise
else:
map(_process_wrapper,
((i, fastq_dir, fc_name, fc_date, config, config_file)
for i in run_info["details"]))
write_metrics(run_info, work_dir, fc_dir, fastq_dir)
def select_upload_files(base, bc_id, fc_dir, analysis_dir):
"""Select fastq, bam alignment and summary files for upload to Galaxy.
"""
fastq_dir = analysis_dir if bc_id else get_fastq_dir(fc_dir)
for fname in glob.glob(os.path.join(fastq_dir, "%s_*fastq.txt" % base)):
yield (fname, os.path.basename(fname))
for summary_file in glob.glob(os.path.join(analysis_dir,
"%s-*summary.pdf" % base)):
yield (summary_file, _name_with_ext(summary_file, "-summary.pdf"))
for bam_file in glob.glob(os.path.join(analysis_dir,
"%s-*sort-dup.bam" % base)):
yield (bam_file, _name_with_ext(bam_file, ".bam"))
for wig_file in glob.glob(os.path.join(analysis_dir,
"%s-*sort.bigwig" % base)):
yield (wig_file, _name_with_ext(wig_file, "-coverage.bigwig"))
# upload any recalibrated BAM files used for SNP calling
found_recal = False
for bam_file in glob.glob(os.path.join(analysis_dir,
"%s-*gatkrecal-realign-sort.bam" % base)):
found_recal = True
yield (bam_file, _name_with_ext(bam_file, "-gatkrecal-realign.bam"))
if not found_recal:
for bam_file in glob.glob(os.path.join(analysis_dir,
"%s-*gatkrecal.bam" % base)):
yield (bam_file, _name_with_ext(bam_file, "-gatkrecal.bam"))
# Genotype files produced by SNP calling
for snp_file in glob.glob(os.path.join(analysis_dir,
"%s-*snp-filter.vcf" % base)):
yield (snp_file, _name_with_ext(bam_file, "-snp-filter.vcf"))
# Effect information on SNPs
for snp_file in glob.glob(os.path.join(analysis_dir,
"%s-*snp-filter-effects.tsv" % base)):
yield (snp_file, _name_with_ext(bam_file, "-snp-effects.tsv"))
def select_upload_files(base, bc_id, fc_dir, analysis_dir):
"""Select fastq, bam alignment and summary files for upload to Galaxy.
"""
# if we have barcodes, update our search name and get local fastq files
if bc_id:
fastq_dir = os.path.join(analysis_dir, "%s_barcode" % base)
base = "%s_%s" % (base, bc_id)
# otherwise, use the original fastq files
else:
fastq_dir = get_fastq_dir(fc_dir)
# fastq, summary and alignment file
for fname in glob.glob(os.path.join(fastq_dir, "%s*_fastq.txt" % base)):
yield (fname, os.path.basename(fname))
for summary_file in glob.glob(os.path.join(analysis_dir, "%s*-summary.pdf" % base)):
yield (summary_file, _name_with_ext(summary_file, "-summary.pdf"))
for bam_file in glob.glob(os.path.join(analysis_dir, "%s*-sort-dup.bam" % base)):
yield (bam_file, _name_with_ext(bam_file, ".bam"))
for wig_file in glob.glob(os.path.join(analysis_dir, "%s*-sort.bigwig" % base)):
yield (wig_file, _name_with_ext(wig_file, "-coverage.bigwig"))
# upload any recalibrated BAM files used for SNP calling
found_recal = False
for bam_file in glob.glob(os.path.join(analysis_dir, "%s*-gatkrecal-realign-sort.bam" % base)):
found_recal = True
yield (bam_file, _name_with_ext(bam_file, "-gatkrecal-realign.bam"))
if not found_recal:
for bam_file in glob.glob(os.path.join(analysis_dir, "%s*-gatkrecal.bam" % base)):
yield (bam_file, _name_with_ext(bam_file, "-gatkrecal.bam"))
# Genotype files produced by SNP calling
for snp_file in glob.glob(os.path.join(analysis_dir, "%s*-snp-filter.vcf" % base)):
yield (snp_file, _name_with_ext(bam_file, "-snp-filter.vcf"))
def _run_toplevel(config, config_file, work_dir, parallel,
fc_dir=None, run_info_yaml=None):
"""
Run toplevel analysis, processing a set of input files.
config_file -- Main YAML configuration file with system parameters
fc_dir -- Directory of fastq files to process
run_info_yaml -- YAML configuration file specifying inputs to process
"""
parallel = log.create_base_logger(config, parallel)
log.setup_local_logging(config, parallel)
fastq_dir, galaxy_dir, config_dir = _get_full_paths(get_fastq_dir(fc_dir)
if fc_dir else None,
config, config_file)
config_file = os.path.join(config_dir, os.path.basename(config_file))
dirs = {"fastq": fastq_dir, "galaxy": galaxy_dir,
"work": work_dir, "flowcell": fc_dir, "config": config_dir}
samples = run_info.organize(dirs, config, run_info_yaml)
pipelines = _pair_lanes_with_pipelines(samples)
final = []
with utils.curdir_tmpdir() as tmpdir:
tempfile.tempdir = tmpdir
for pipeline, pipeline_items in pipelines.items():
pipeline_items = _add_provenance(pipeline_items, dirs, parallel, config)
versioncheck.testall(pipeline_items)
for xs in pipeline.run(config, config_file, parallel, dirs, pipeline_items):
if len(xs) == 1:
upload.from_sample(xs[0])
final.append(xs[0])
def select_upload_files(base, bc_id, fc_dir, analysis_dir, config, fname_out=None):
"""Select fastq, bam alignment and summary files for upload to Galaxy.
"""
def _name_with_ext(orig_file, ext):
"""Return a normalized filename without internal processing names.
Use specific base out filename if specific, allowing configuration
named output files.
"""
if fname_out is None:
base = os.path.basename(orig_file).split("-")[0]
else:
base = fname_out
for extra in ["_trim"]:
if base.endswith(extra):
base = base[:-len(extra)]
return "%s%s" % (base, ext)
base_glob = _dir_glob(base, analysis_dir)
# Configurable upload of fastq files -- BAM provide same information, compacted
if config["algorithm"].get("upload_fastq", True):
# look for fastq files in a barcode directory or the main fastq directory
bc_base = base.rsplit("_", 1)[0] if bc_id else base
bc_dir = os.path.join(analysis_dir, "%s_barcode" % bc_base)
fastq_glob = "%s_*fastq.txt" % base
found_fastq = False
for fname in glob.glob(os.path.join(bc_dir, fastq_glob)):
found_fastq = True
yield (fname, os.path.basename(fname))
if not found_fastq:
fastq_dir = get_fastq_dir(fc_dir)
for fname in glob.glob(os.path.join(fastq_dir, fastq_glob)):
yield (fname, os.path.basename(fname))
for summary_file in base_glob("summary.pdf"):
yield (summary_file, _name_with_ext(summary_file, "-summary.pdf"))
for wig_file in base_glob(".bigwig"):
yield (wig_file, _name_with_ext(wig_file, "-coverage.bigwig"))
# upload BAM files, preferring recalibrated and realigned files
found_bam = False
for orig_ext, new_ext in [("gatkrecal-realign-dup.bam", "-gatkrecal-realign.bam"),
("gatkrecal-realign.bam", "-gatkrecal-realign.bam"),
("gatkrecal.bam", "-gatkrecal.bam"),
("sort-dup.bam", ".bam"),
("sort.bam", ".bam")]:
if not found_bam:
for bam_file in base_glob(orig_ext):
yield (bam_file, _name_with_ext(bam_file, new_ext))
found_bam = True
# Genotype files produced by SNP calling
found = False
for orig_ext, new_ext in [("variants-combined-annotated.vcf", "-variants.vcf"),
("variants-*-annotated.vcf", "-variants.vcf")]:
if not found:
for snp_file in base_glob(orig_ext):
yield (snp_file, _name_with_ext(bam_file, new_ext))
found = True
# Effect information on SNPs
for snp_file in base_glob("variants-*-effects.tsv"):
yield (snp_file, _name_with_ext(bam_file, "-variants-effects.tsv"))
def _generate_fastq(fc_dir):
"""Generate fastq files for the current flowcell.
"""
fc_name, fc_date = get_flowcell_info(fc_dir)
short_fc_name = "%s_%s" % (fc_date, fc_name)
fastq_dir = get_fastq_dir(fc_dir)
if not fastq_dir == fc_dir and not os.path.exists(fastq_dir):
with utils.chdir(os.path.split(fastq_dir)[0]):
lanes = sorted(list(set([f.split("_")[1] for f in
glob.glob("*qseq.txt")])))
cl = ["solexa_qseq_to_fastq.py", short_fc_name,
",".join(lanes)]
subprocess.check_call(cl)
return fastq_dir
def run_main(config,
config_file,
work_dir,
parallel,
fc_dir=None,
run_info_yaml=None):
"""Run toplevel analysis, processing a set of input files.
config_file -- Main YAML configuration file with system parameters
fc_dir -- Directory of fastq files to process
run_info_yaml -- YAML configuration file specifying inputs to process
"""
setup_logging(config)
fc_name, fc_date, run_info = get_run_info(fc_dir, config, run_info_yaml)
fastq_dir, galaxy_dir, config_dir = _get_full_paths(
get_fastq_dir(fc_dir) if fc_dir else None, config, config_file)
config_file = os.path.join(config_dir, os.path.basename(config_file))
dirs = {
"fastq": fastq_dir,
"galaxy": galaxy_dir,
"work": work_dir,
"flowcell": fc_dir,
"config": config_dir
}
config = _set_resources(parallel, config)
run_parallel = parallel_runner(parallel, dirs, config, config_file)
# process each flowcell lane
run_items = add_multiplex_across_lanes(run_info["details"], dirs["fastq"],
fc_name)
lanes = ((info, fc_name, fc_date, dirs, config) for info in run_items)
lane_items = run_parallel("process_lane", lanes)
align_items = run_parallel("process_alignment", lane_items)
# process samples, potentially multiplexed across multiple lanes
samples = organize_samples(align_items, dirs, config_file)
samples = run_parallel("merge_sample", samples)
samples = run_parallel("prep_recal", samples)
samples = recalibrate.parallel_write_recal_bam(samples, run_parallel)
samples = parallel_realign_sample(samples, run_parallel)
samples = parallel_variantcall(samples, run_parallel)
samples = run_parallel("postprocess_variants", samples)
samples = combine_multiple_callers(samples)
samples = run_parallel("detect_sv", samples)
samples = run_parallel("combine_calls", samples)
run_parallel("process_sample", samples)
run_parallel("generate_bigwig", samples, {"programs": ["ucsc_bigwig"]})
write_project_summary(samples)
write_metrics(run_info, fc_name, fc_date, dirs)
def _normalize_files(item, fc_dir):
"""Ensure the files argument is a list of absolute file names.
Handles BAM, single and paired end fastq.
"""
files = item.get("files")
if files:
if isinstance(files, basestring):
files = [files]
if fc_dir:
fastq_dir = get_fastq_dir(fc_dir)
files = [
x if os.path.isabs(x) else os.path.normpath(
os.path.join(fastq_dir, x)) for x in files
]
item["files"] = files
return item
def _normalize_files(item, fc_dir):
"""Ensure the files argument is a list of absolute file names.
Handles BAM, single and paired end fastq.
"""
files = item.get("files")
if files:
if isinstance(files, basestring):
files = [files]
if fc_dir:
fastq_dir = get_fastq_dir(fc_dir)
else:
fastq_dir = os.getcwd()
files = [x if os.path.isabs(x) else os.path.normpath(os.path.join(fastq_dir, x))
for x in files]
item["files"] = files
return item
def _generate_fastq(fc_dir, config):
"""Generate fastq files for the current flowcell.
"""
fc_name, fc_date = get_flowcell_info(fc_dir)
short_fc_name = "%s_%s" % (fc_date, fc_name)
fastq_dir = get_fastq_dir(fc_dir)
basecall_dir = os.path.split(fastq_dir)[0]
if not fastq_dir == fc_dir and not os.path.exists(fastq_dir):
log.info("Generating fastq files for %s" % fc_dir)
with utils.chdir(basecall_dir):
lanes = sorted(
list(set([f.split("_")[1] for f in glob.glob("*qseq.txt")])))
cl = ["solexa_qseq_to_fastq.py", short_fc_name, ",".join(lanes)]
log.info("Converting qseq to fastq on all lanes.")
subprocess.check_call(cl)
log.info("Qseq to fastq conversion completed.")
return fastq_dir
def _generate_fastq(fc_dir, config):
"""Generate fastq files for the current flowcell.
"""
fc_name, fc_date = get_flowcell_info(fc_dir)
short_fc_name = "%s_%s" % (fc_date, fc_name)
fastq_dir = get_fastq_dir(fc_dir)
basecall_dir = os.path.split(fastq_dir)[0]
if not fastq_dir == fc_dir and not os.path.exists(fastq_dir):
log.info("Generating fastq files for %s" % fc_dir)
with utils.chdir(basecall_dir):
lanes = sorted(list(set([f.split("_")[1] for f in
glob.glob("*qseq.txt")])))
cl = ["solexa_qseq_to_fastq.py", short_fc_name,
",".join(lanes)]
log.info("Converting qseq to fastq on all lanes.")
subprocess.check_call(cl)
log.info("Qseq to fastq conversion completed.")
return fastq_dir
def main(config_file, fc_dir):
work_dir = os.getcwd()
config = load_config(config_file)
galaxy_api = GalaxyApiAccess(config['galaxy_url'], config['galaxy_api_key'])
fc_name, fc_date = get_flowcell_info(fc_dir)
run_info = galaxy_api.run_details(fc_name)
fastq_dir = get_fastq_dir(fc_dir)
if config["algorithm"]["num_cores"] > 1:
pool = Pool(config["algorithm"]["num_cores"])
try:
pool.map(_process_wrapper,
((i, fastq_dir, fc_name, fc_date, config, config_file)
for i in run_info["details"]))
except:
pool.terminate()
raise
else:
map(_process_wrapper,
((i, fastq_dir, fc_name, fc_date, config, config_file)
for i in run_info["details"]))
def main(config_file, fc_dir):
work_dir = os.getcwd()
config = load_config(config_file)
galaxy_api = GalaxyApiAccess(config['galaxy_url'], config['galaxy_api_key'])
fc_name, fc_date = get_flowcell_info(fc_dir)
run_info = galaxy_api.run_details(fc_name)
fastq_dir = get_fastq_dir(fc_dir)
if config["algorithm"]["num_cores"] > 1:
pool = Pool(config["algorithm"]["num_cores"])
try:
pool.map(_process_wrapper,
((i, fastq_dir, fc_name, fc_date, config, config_file)
for i in run_info["details"]))
except:
pool.terminate()
raise
else:
map(_process_wrapper,
((i, fastq_dir, fc_name, fc_date, config, config_file)
for i in run_info["details"]))
def main(config_file, fc_dir, run_info_yaml=None):
work_dir = os.getcwd()
with open(config_file) as in_handle:
config = yaml.load(in_handle)
if run_info_yaml:
with open(run_info_yaml) as in_handle:
run_details = yaml.load(in_handle)
run_info = dict(details=run_details, run_id="")
else:
galaxy_api = GalaxyApiAccess(config['galaxy_url'], config['galaxy_api_key'])
run_info = galaxy_api.run_details(fc_name)
fc_name, fc_date = get_flowcell_info(fc_dir)
run_items = _add_multiplex_to_control(run_info["details"])
fastq_dir = get_fastq_dir(fc_dir)
align_dir = os.path.join(work_dir, "alignments")
# process each flowcell lane
pool = (Pool(config["algorithm"]["num_cores"])
if config["algorithm"]["num_cores"] > 1 else None)
map_fn = pool.map if pool else map
try:
map_fn(_process_lane_wrapper,
((i, fastq_dir, fc_name, fc_date, align_dir, config, config_file)
for i in run_items))
except:
if pool:
pool.terminate()
raise
# process samples, potentially multiplexed across multiple lanes
sample_files, sample_fastq, sample_info = organize_samples(align_dir,
fastq_dir, work_dir, fc_name, fc_date, run_items)
try:
map_fn(_process_sample_wrapper,
((name, sample_fastq[name], sample_info[name], bam_files, work_dir,
config, config_file) for name, bam_files in sample_files))
except:
if pool:
pool.terminate()
raise
write_metrics(run_info, work_dir, fc_dir, fc_name, fc_date, fastq_dir)
def run_main(config,
config_file,
work_dir,
parallel,
fc_dir=None,
run_info_yaml=None):
"""
Run toplevel analysis, processing a set of input files.
config_file -- Main YAML configuration file with system parameters
fc_dir -- Directory of fastq files to process
run_info_yaml -- YAML configuration file specifying inputs to process
"""
setup_logging(config)
fc_name, fc_date, run_info = get_run_info(fc_dir, config, run_info_yaml)
fastq_dir, galaxy_dir, config_dir = _get_full_paths(
get_fastq_dir(fc_dir) if fc_dir else None, config, config_file)
config_file = os.path.join(config_dir, os.path.basename(config_file))
dirs = {
"fastq": fastq_dir,
"galaxy": galaxy_dir,
"work": work_dir,
"flowcell": fc_dir,
"config": config_dir
}
run_parallel = parallel_runner(parallel, dirs, config, config_file)
# process each flowcell lane
run_items = add_multiplex_across_lanes(run_info["details"], dirs["fastq"],
fc_name)
lanes = ((info, fc_name, fc_date, dirs, config) for info in run_items)
lane_items = lane.process_all_lanes(lanes, run_parallel)
pipelines = _pair_lanes_with_pipelines(lane_items)
for pipeline, pipeline_items in pipelines.items():
pipeline_items = _add_provenance(pipeline_items, dirs, config)
for xs in pipeline.run(config, config_file, run_parallel, dirs,
pipeline_items):
assert len(xs) == 1
upload.from_sample(xs[0])
qcsummary.write_metrics(run_info, fc_name, fc_date, dirs)
def select_upload_files(base, bc_id, fc_dir, analysis_dir, config):
"""Select fastq, bam alignment and summary files for upload to Galaxy.
"""
base_glob = _dir_glob(base, analysis_dir)
# Configurable upload of fastq files -- BAM provide same information, compacted
if config["algorithm"].get("upload_fastq", True):
# look for fastq files in a barcode directory or the main fastq directory
bc_base = base.rsplit("_", 1)[0] if bc_id else base
bc_dir = os.path.join(analysis_dir, "%s_barcode" % bc_base)
fastq_glob = "%s_*fastq.txt" % base
found_fastq = False
for fname in glob.glob(os.path.join(bc_dir, fastq_glob)):
found_fastq = True
yield (fname, os.path.basename(fname))
if not found_fastq:
fastq_dir = get_fastq_dir(fc_dir)
for fname in glob.glob(os.path.join(fastq_dir, fastq_glob)):
yield (fname, os.path.basename(fname))
for summary_file in base_glob("summary.pdf"):
yield (summary_file, _name_with_ext(summary_file, "-summary.pdf"))
for wig_file in base_glob(".bigwig"):
yield (wig_file, _name_with_ext(wig_file, "-coverage.bigwig"))
# upload BAM files, preferring recalibrated and realigned files
found_recal = False
for bam_file in base_glob("gatkrecal-realign-dup.bam"):
found_recal = True
yield (bam_file, _name_with_ext(bam_file, "-gatkrecal-realign.bam"))
if not found_recal:
for bam_file in base_glob("gatkrecal.bam"):
found_recal = True
yield (bam_file, _name_with_ext(bam_file, "-gatkrecal.bam"))
if not found_recal:
for bam_file in base_glob("sort-dup.bam"):
yield (bam_file, _name_with_ext(bam_file, ".bam"))
# Genotype files produced by SNP calling
for snp_file in base_glob("variants-combined-annotated.vcf"):
yield (snp_file, _name_with_ext(bam_file, "-variants.vcf"))
# Effect information on SNPs
for snp_file in base_glob("variants-combined-effects.tsv"):
yield (snp_file, _name_with_ext(bam_file, "-variants-effects.tsv"))
def select_upload_files(base, bc_id, fc_dir, analysis_dir, config):
"""Select fastq, bam alignment and summary files for upload to Galaxy.
"""
base_glob = _dir_glob(base, analysis_dir)
# Configurable upload of fastq files -- BAM provide same information, compacted
if config["algorithm"].get("upload_fastq", True):
# look for fastq files in a barcode directory or the main fastq directory
bc_base = base.rsplit("_", 1)[0] if bc_id else base
bc_dir = os.path.join(analysis_dir, "%s_barcode" % bc_base)
fastq_glob = "%s_*fastq.txt" % base
found_fastq = False
for fname in glob.glob(os.path.join(bc_dir, fastq_glob)):
found_fastq = True
yield (fname, os.path.basename(fname))
if not found_fastq:
fastq_dir = get_fastq_dir(fc_dir)
for fname in glob.glob(os.path.join(fastq_dir, fastq_glob)):
yield (fname, os.path.basename(fname))
for summary_file in base_glob("summary.pdf"):
yield (summary_file, _name_with_ext(summary_file, "-summary.pdf"))
for bam_file in base_glob("sort-dup.bam"):
yield (bam_file, _name_with_ext(bam_file, ".bam"))
for wig_file in base_glob("sort.bigwig"):
yield (wig_file, _name_with_ext(wig_file, "-coverage.bigwig"))
# upload any recalibrated BAM files used for SNP calling
found_recal = False
for bam_file in base_glob("gatkrecal-realign-sort.bam"):
found_recal = True
yield (bam_file, _name_with_ext(bam_file, "-gatkrecal-realign.bam"))
if not found_recal:
for bam_file in base_glob("gatkrecal.bam"):
yield (bam_file, _name_with_ext(bam_file, "-gatkrecal.bam"))
# Genotype files produced by SNP calling
for snp_file in base_glob("snp-filter.vcf"):
yield (snp_file, _name_with_ext(bam_file, "-snp-filter.vcf"))
# Effect information on SNPs
for snp_file in base_glob("snp-filter-effects.tsv"):
yield (snp_file, _name_with_ext(bam_file, "-snp-effects.tsv"))
def run_main(config, config_file, work_dir, parallel,
fc_dir=None, run_info_yaml=None):
"""Run toplevel analysis, processing a set of input files.
config_file -- Main YAML configuration file with system parameters
fc_dir -- Directory of fastq files to process
run_info_yaml -- YAML configuration file specifying inputs to process
"""
setup_logging(config)
fc_name, fc_date, run_info = get_run_info(fc_dir, config, run_info_yaml)
fastq_dir, galaxy_dir, config_dir = _get_full_paths(get_fastq_dir(fc_dir) if fc_dir else None,
config, config_file)
config_file = os.path.join(config_dir, os.path.basename(config_file))
dirs = {"fastq": fastq_dir, "galaxy": galaxy_dir,
"work": work_dir, "flowcell": fc_dir, "config": config_dir}
config = _set_resources(parallel, config)
run_parallel = parallel_runner(parallel, dirs, config, config_file)
# process each flowcell lane
run_items = add_multiplex_across_lanes(run_info["details"], dirs["fastq"], fc_name)
lanes = ((info, fc_name, fc_date, dirs, config) for info in run_items)
lane_items = run_parallel("process_lane", lanes)
align_items = run_parallel("process_alignment", lane_items)
# process samples, potentially multiplexed across multiple lanes
samples = organize_samples(align_items, dirs, config_file)
samples = run_parallel("merge_sample", samples)
samples = run_parallel("prep_recal", samples)
samples = recalibrate.parallel_write_recal_bam(samples, run_parallel)
samples = parallel_realign_sample(samples, run_parallel)
samples = parallel_variantcall(samples, run_parallel)
samples = run_parallel("postprocess_variants", samples)
samples = combine_multiple_callers(samples)
samples = run_parallel("detect_sv", samples)
samples = run_parallel("combine_calls", samples)
run_parallel("process_sample", samples)
run_parallel("generate_bigwig", samples, {"programs": ["ucsc_bigwig"]})
write_project_summary(samples)
write_metrics(run_info, fc_name, fc_date, dirs)
def run_main(config, config_file, fc_dir, run_info_yaml):
work_dir = os.getcwd()
fc_name, fc_date = get_flowcell_info(fc_dir)
if run_info_yaml and os.path.exists(run_info_yaml):
log.info("Found YAML samplesheet, using %s instead of Galaxy API" %
run_info_yaml)
with open(run_info_yaml) as in_handle:
run_details = yaml.load(in_handle)
run_info = dict(details=run_details, run_id="")
else:
log.info("Fetching run details from Galaxy instance")
galaxy_api = GalaxyApiAccess(config['galaxy_url'],
config['galaxy_api_key'])
run_info = galaxy_api.run_details(fc_name, fc_date)
fastq_dir = get_fastq_dir(fc_dir)
run_items = _add_multiplex_across_lanes(run_info["details"], fastq_dir,
fc_name)
align_dir = os.path.join(work_dir, "alignments")
# process each flowcell lane
with utils.cpmap(config["algorithm"]["num_cores"]) as cpmap:
for _ in cpmap(
process_lane,
((i, fastq_dir, fc_name, fc_date, align_dir, config, config_file)
for i in run_items)):
pass
# process samples, potentially multiplexed across multiple lanes
sample_files, sample_fastq, sample_info = organize_samples(
align_dir, fastq_dir, work_dir, fc_name, fc_date, run_items)
with utils.cpmap(config["algorithm"]["num_cores"]) as cpmap:
for _ in cpmap(process_sample,
((name, sample_fastq[name], sample_info[name],
bam_files, work_dir, config, config_file)
for name, bam_files in sample_files)):
pass
write_metrics(run_info, work_dir, fc_dir, fc_name, fc_date, fastq_dir)
def run_main(config, config_file, fc_dir, work_dir, run_info_yaml):
_record_sw_versions(config, os.path.join(work_dir, "bcbb_software_versions.txt"))
prog = RecordProgress(work_dir)
to_compress = set()
prog.progress("analysis_start")
align_dir = os.path.join(work_dir, "alignments")
run_module = "bcbio.distributed"
fc_name, fc_date, run_info = get_run_info(fc_dir, config, run_info_yaml)
fastq_dir, galaxy_dir, config_dir = _get_full_paths(get_fastq_dir(fc_dir),
config, config_file)
config_file = os.path.join(config_dir, os.path.basename(config_file))
dirs = {"fastq": fastq_dir, "galaxy": galaxy_dir, "align": align_dir,
"work": work_dir, "flowcell": fc_dir, "config": config_dir}
run_parallel = parallel_runner(run_module, dirs, config, config_file)
run_items = add_multiplex_across_lanes(run_info["details"], dirs["fastq"], fc_name)
lanes = ((info, fc_name, fc_date, dirs, config) for info in run_items)
lane_items = run_parallel("process_lane", lanes)
_add_to_compress(to_compress, lane_items, 'lane_items')
prog.dummy()
prog.progress("process_lane")
# Remove spiked in controls, contaminants etc.
lane_items = run_parallel("remove_contaminants", lane_items)
_add_to_compress(to_compress, lane_items, 'lane_items')
prog.dummy()
prog.progress("remove_contaminants")
align_items = run_parallel("process_alignment", lane_items)
_add_to_compress(to_compress, align_items, 'align_items')
prog.dummy()
prog.progress("process_alignment")
# process samples, potentially multiplexed across multiple lanes
samples = organize_samples(align_items, dirs, config_file)
samples = run_parallel("merge_sample", samples)
_add_to_compress(to_compress, samples, 'samples')
prog.dummy()
prog.progress("merge_sample")
samples = run_parallel("mark_duplicates_sample", samples)
_add_to_compress(to_compress, samples, 'samples')
prog.dummy()
prog.progress("mark_duplicates_sample")
run_parallel("screen_sample_contaminants", samples)
prog.dummy()
prog.progress("screen_sample_contaminants")
samples = run_parallel("recalibrate_sample", samples)
_add_to_compress(to_compress, samples, 'samples')
prog.dummy()
prog.progress("recalibrate_sample")
samples = parallel_realign_sample(samples, run_parallel)
_add_to_compress(to_compress, samples, 'samples')
prog.dummy()
prog.progress("realign_sample")
samples = parallel_variantcall(samples, run_parallel)
_add_to_compress(to_compress, samples, 'samples')
prog.dummy()
prog.progress("variantcall")
samples = run_parallel("detect_sv", samples)
_add_to_compress(to_compress, samples, 'samples')
prog.dummy()
prog.progress("detect_sv")
samples = run_parallel("process_sample", samples)
_add_to_compress(to_compress, samples, 'samples')
prog.dummy()
prog.progress("process_sample")
samples = run_parallel("generate_bigwig", samples, {"programs": ["ucsc_bigwig"]})
_add_to_compress(to_compress, samples, 'samples')
prog.dummy()
prog.progress("generate_bigwig")
write_project_summary(samples)
write_metrics(run_info, fc_name, fc_date, dirs)
prog.dummy()
prog.progress("write_metrics")
# Compress all files in to_compress
if config['algorithm'].get('compress_files', True):
sizes = run_parallel("compress_files", [[[cf]] for cf in to_compress])
before = sum([s[0] for s in sizes])
after = sum([s[1] for s in sizes])
logger.info("Space used by the files before compressing (in bytes): " \
+ str(before))
logger.info("Space used by the files after compressing (in bytes): " \
+ str(after))
logger.info("Saved space (in bytes): " + str(before - after))
def run_main(config, config_file, fc_dir, work_dir, run_info_yaml):
_record_sw_versions(config, os.path.join(work_dir, "bcbb_software_versions.txt"))
prog = utils.RecordProgress(work_dir)
to_compress = set()
prog.progress("analysis_start")
align_dir = os.path.join(work_dir, "alignments")
run_module = "bcbio.distributed"
fc_name, fc_date, run_info = get_run_info(fc_dir, config, run_info_yaml)
fastq_dir, galaxy_dir, config_dir = _get_full_paths(get_fastq_dir(fc_dir),
config, config_file)
config_file = os.path.join(config_dir, os.path.basename(config_file))
dirs = {"fastq": fastq_dir, "galaxy": galaxy_dir, "align": align_dir,
"work": work_dir, "flowcell": fc_dir, "config": config_dir}
run_parallel = parallel_runner(run_module, dirs, config, config_file)
run_items = add_multiplex_across_lanes(run_info["details"], dirs["fastq"], fc_name)
lanes = ((info, fc_name, fc_date, dirs, config) for info in run_items)
lane_items = run_parallel("process_lane", lanes)
[to_compress.add(f) for f in lane_items[0][0:2]]
prog.progress("process_lane")
# upload the sequencing report to Google Docs
# will skip this for now and rely on external mechanism for uploading this data
#gdocs_indicator = os.path.join(work_dir, "gdocs_report_complete.txt")
#if not os.path.exists(gdocs_indicator) \
#and queue_report(fc_date, fc_name, os.path.abspath(run_info_yaml), dirs, config, config_file):
# utils.touch_file(gdocs_indicator)
# Remove spiked in controls, contaminants etc.
lane_items = run_parallel("remove_contaminants", lane_items)
[to_compress.add(f) for f in lane_items[0][0:2]]
prog.progress("remove_contaminants")
align_items = run_parallel("process_alignment", lane_items)
[to_compress.add(f) for f in align_items[0]['fastq']]
prog.progress("process_alignment")
# process samples, potentially multiplexed across multiple lanes
samples = organize_samples(align_items, dirs, config_file)
samples = run_parallel("merge_sample", samples)
to_compress.add(samples[0][0]['fastq1'])
to_compress.add(samples[0][0]['fastq2'])
prog.progress("merge_sample")
samples = run_parallel("mark_duplicates_sample", samples)
to_compress.add(samples[0][0]['fastq1'])
to_compress.add(samples[0][0]['fastq2'])
prog.progress("mark_duplicates_sample")
run_parallel("screen_sample_contaminants", samples)
prog.progress("screen_sample_contaminants")
samples = run_parallel("recalibrate_sample", samples)
prog.progress("recalibrate_sample")
samples = parallel_realign_sample(samples, run_parallel)
prog.progress("realign_sample")
samples = parallel_variantcall(samples, run_parallel)
prog.progress("variantcall")
samples = run_parallel("detect_sv", samples)
prog.progress("detect_sv")
samples = run_parallel("process_sample", samples)
prog.progress("process_sample")
samples = run_parallel("generate_bigwig", samples, {"programs": ["ucsc_bigwig"]})
prog.progress("generate_bigwig")
write_project_summary(samples)
write_metrics(run_info, fc_name, fc_date, dirs)
prog.progress("write_metrics")
# Write statusdb metrics
# will skip this for now and rely on external mechanism for uploading this data
#report_to_statusdb(fc_name, fc_date, run_info_yaml, dirs, config)
#Compress all files in to_compress
if config['algorithm'].get('compress_files', True):
(before, after) = utils.compress_files(to_compress)
logger.info("Space used by the files before compressing (in bytes): " \
+ str(before))
logger.info("Space used by the files after compressing (in bytes): " \
+ str(after))
logger.info("Saved space (in bytes): " + str(before - after))
def select_upload_files(base,
bc_id,
fc_dir,
analysis_dir,
config,
fname_out=None):
"""Select fastq, bam alignment and summary files for upload to Galaxy.
"""
def _name_with_ext(orig_file, ext):
"""Return a normalized filename without internal processing names.
Use specific base out filename if specific, allowing configuration
named output files.
"""
if fname_out is None:
base = os.path.basename(orig_file).split("-")[0]
else:
base = fname_out
for extra in ["_trim"]:
if base.endswith(extra):
base = base[:-len(extra)]
return "%s%s" % (base, ext)
base_glob = _dir_glob(base, analysis_dir)
# Configurable upload of fastq files -- BAM provide same information, compacted
if config["algorithm"].get("upload_fastq", True):
# look for fastq files in a barcode directory or the main fastq directory
bc_base = base.rsplit("_", 1)[0] if bc_id else base
bc_dir = os.path.join(analysis_dir, "%s_barcode" % bc_base)
fastq_glob = "%s_*fastq.txt" % base
found_fastq = False
for fname in glob.glob(os.path.join(bc_dir, fastq_glob)):
found_fastq = True
yield (fname, os.path.basename(fname))
if not found_fastq:
fastq_dir = get_fastq_dir(fc_dir)
for fname in glob.glob(os.path.join(fastq_dir, fastq_glob)):
yield (fname, os.path.basename(fname))
for summary_file in base_glob("summary.pdf"):
yield (summary_file, _name_with_ext(summary_file, "-summary.pdf"))
for wig_file in base_glob(".bigwig"):
yield (wig_file, _name_with_ext(wig_file, "-coverage.bigwig"))
# upload BAM files, preferring recalibrated and realigned files
found_bam = False
for orig_ext, new_ext in [
("gatkrecal-realign-dup.bam", "-gatkrecal-realign.bam"),
("gatkrecal-realign.bam", "-gatkrecal-realign.bam"),
("gatkrecal.bam", "-gatkrecal.bam"), ("sort-dup.bam", ".bam"),
("sort.bam", ".bam")
]:
if not found_bam:
for bam_file in base_glob(orig_ext):
yield (bam_file, _name_with_ext(bam_file, new_ext))
found_bam = True
# Genotype files produced by SNP calling
found = False
for orig_ext, new_ext in [("variants-combined-annotated.vcf",
"-variants.vcf"),
("variants-*-annotated.vcf", "-variants.vcf")]:
if not found:
for snp_file in base_glob(orig_ext):
yield (snp_file, _name_with_ext(bam_file, new_ext))
found = True
# Effect information on SNPs
for snp_file in base_glob("variants-*-effects.tsv"):
yield (snp_file, _name_with_ext(bam_file, "-variants-effects.tsv"))