def join(args, outs, chunk_defs, chunk_outs):
if args.skip or args.is_multi_genome:
return
chunk_out = chunk_outs[0]
cr_utils.copy(chunk_out.pca_h5, outs.pca_h5)
cr_utils.copytree(chunk_out.pca_csv, outs.pca_csv)
def main(args, outs):
if args.skip:
return
if args.random_seed is not None:
np.random.seed(args.random_seed)
# detect barnyard
genomes = cr_matrix.GeneBCMatrices.load_genomes_from_h5(args.matrix_h5)
if len(genomes) > 1:
outs.is_multi_genome = True
cr_utils.copy(args.matrix_h5, outs.preprocessed_matrix_h5)
return
else:
outs.is_multi_genome = False
genome = genomes[0]
matrix = cr_matrix.GeneBCMatrices.load_h5(
args.matrix_h5).get_matrix(genome)
matrix = cr_matrix.GeneBCMatrix.preprocess_matrix(
matrix,
num_bcs=args.num_bcs,
use_bcs=args.use_bcs,
use_genes=args.use_genes,
force_cells=args.force_cells)
gbm = cr_matrix.GeneBCMatrices()
gbm.matrices[genome] = matrix
matrix_attrs = cr_matrix.get_matrix_attrs(args.matrix_h5)
gbm.save_h5(outs.preprocessed_matrix_h5, extra_attrs=matrix_attrs)
def join(args, outs, chunk_defs, chunk_outs):
if args.skip:
return
chunk_out = chunk_outs[0]
cr_utils.copy(chunk_out.preprocessed_matrix_h5,
outs.preprocessed_matrix_h5)
outs.is_multi_genome = chunk_out.is_multi_genome
def join(args, outs, chunk_defs, chunk_outs):
if args.skip or not args.is_multi_genome:
return
chunk_out = chunk_outs[0]
cr_utils.copy(chunk_out.multi_genome_summary, outs.multi_genome_summary)
cr_utils.copytree(chunk_out.multi_genome_csv, outs.multi_genome_csv)
cr_utils.copytree(chunk_out.multi_genome_json, outs.multi_genome_json)
def main(args, outs):
parsed = parse_parameters(args.params_csv)
for param in ANALYSIS_PARAMS:
if param in parsed:
setattr(outs, param, parsed[param])
else:
setattr(outs, param, None)
if args.params_csv is not None:
cr_utils.copy(args.params_csv, outs.params_csv)
def join(args, outs, chunk_defs, chunk_outs):
cr_utils.copy(args.extract_reads_summary, outs.summary)
cr_utils.copy(args.barcode_counts, outs.barcode_counts)
outs.gem_groups = args.gem_groups
outs.read_groups = args.read_groups
outs.align = args.align
outs.bam_comments = args.bam_comments
outs.read1s = [co.read1s for co in chunk_outs]
outs.read2s = [co.read2s for co in chunk_outs]
def get_gem_group_index_json(args, outs):
if args.gem_group_index_json:
cr_utils.copy(args.gem_group_index_json, outs.gem_group_index_json)
else:
generated_index = cr_matrix.get_gem_group_index(
args.filtered_gene_bc_matrices_h5)
if generated_index:
with open(outs.gem_group_index_json, 'w') as outfile:
tk_json.dump_numpy({"gem_group_index": generated_index},
outfile)
return outs.gem_group_index_json
def write_genome_fasta(self, out_fasta_fn):
if len(self.genomes) > 1:
with open(out_fasta_fn, 'w') as f:
for genome_prefix, in_fasta_fn in itertools.izip(self.genome_prefixes, self.in_fasta_fns):
with open(in_fasta_fn, 'r') as g:
for line in g:
line = line.strip()
if line.startswith('>'):
line = '>' + genome_prefix + '_' + line[1:]
f.write(line + '\n')
else:
cr_utils.copy(self.in_fasta_fns[0], out_fasta_fn)
def main(args, outs):
if args.read1 is not None:
# Ensure same extension
out_path, _ = cr_utils.splitexts(outs.read1s)
_, in_ext = cr_utils.splitexts(args.read1)
outs.read1s = out_path + in_ext
cr_utils.copy(args.read1, outs.read1s)
if args.read2 is not None:
out_path, _ = cr_utils.splitexts(outs.read2s)
_, in_ext = cr_utils.splitexts(args.read2)
outs.read2s = out_path + in_ext
cr_utils.copy(args.read2, outs.read2s)
def join(args, outs, chunk_defs, chunk_outs):
summary_files = [
args.reads_summary,
args.filter_umis_summary,
args.filter_barcodes_summary,
args.trim_reads_summary,
args.filter_reads_summary,
args.filter_contigs_summary,
args.report_contigs_summary,
args.report_contig_alignments_summary,
args.raw_consensus_summary,
args.group_clonotypes_summary,
]
summary_files = [sum_file for sum_file in summary_files if not sum_file is None]
cr_report.merge_jsons(summary_files, outs.metrics_summary_json)
# Copy barcode summary h5
if args.barcode_summary:
cr_utils.copy(args.barcode_summary, outs.barcode_summary)
# Copy cell barcodes
if args.cell_barcodes:
cr_utils.copy(args.cell_barcodes, outs.cell_barcodes)
# Copy barcode support
if args.barcode_support:
cr_utils.copy(args.barcode_support, outs.barcode_support)
# Copy barcode umi summary
if args.barcode_umi_summary:
cr_utils.copy(args.barcode_umi_summary, outs.barcode_umi_summary)
# Copy umi info
if args.umi_info:
cr_utils.copy(args.umi_info, outs.umi_info)
sample_data_paths = cr_webshim_data.SampleDataPaths(
summary_path=outs.metrics_summary_json,
barcode_summary_path=args.barcode_summary,
vdj_clonotype_summary_path=args.clonotype_summary,
vdj_barcode_support_path=args.barcode_support,
)
sample_properties = cr_webshim.get_sample_properties(args.sample_id, args.sample_desc, [], version=martian.get_pipelines_version())
sample_data = cr_webshim.load_sample_data(sample_properties, sample_data_paths)
if args.barcode_whitelist is not None:
cr_webshim.build_web_summary_html(outs.web_summary, sample_properties, sample_data, PIPELINE_VDJ,
alerts_output_filename=outs.alerts)
cr_webshim.build_metrics_summary_csv(outs.metrics_summary_csv, sample_properties, sample_data, PIPELINE_VDJ)
def join(args, outs, chunk_defs, chunk_outs):
# Copy files from single chunk to join
for out_name in ['summary',
'contig_annotations',
'filtered_contig_fasta',
'filtered_contig_fastq',
]:
src = getattr(chunk_outs[0], out_name)
dest = getattr(outs, out_name)
if os.path.isfile(src):
cr_utils.copy(src, dest)
else:
setattr(outs, out_name, None)
def join(args, outs, chunk_defs, chunk_outs):
chunk_out = chunk_outs[0]
cr_utils.copy(chunk_out.web_summary, outs.web_summary)
cr_utils.copy(chunk_out.alerts, outs.alerts)
cr_utils.copy(chunk_out.metrics_summary_json, outs.metrics_summary_json)
cr_utils.copy(chunk_out.metrics_summary_csv, outs.metrics_summary_csv)
def join(args, outs, chunk_defs, chunk_outs):
if args.skip:
outs.analysis = None
outs.analysis_csv = None
outs.summary = None
return
chunk_out = chunk_outs[0]
cr_utils.copytree(chunk_out.analysis, outs.analysis)
cr_utils.copytree(chunk_out.analysis_csv, outs.analysis_csv)
if args.is_multi_genome:
cr_utils.copy(args.multi_genome_summary, outs.summary)
else:
outs.summary = None
def main(args, outs):
# NOOP if no vdj ref path specified
if args.vdj_reference_path is None:
outs.recombinome = None
outs.recombinome_index = None
return
fasta_filename = vdj_reference.get_vdj_reference_fasta(
args.vdj_reference_path)
cr_utils.copy(fasta_filename, outs.recombinome)
os.makedirs(outs.recombinome_index)
# Build a bowtie2 index
subprocess.check_call([
'bowtie2-build', outs.recombinome,
os.path.join(outs.recombinome_index, 'recombinome')
])
def join(args, outs, chunk_defs, chunk_outs):
downsample = chunk_defs[0].downsample
downsample_map = chunk_defs[0].downsample_map
if downsample and len(downsample_map) > 1:
input_h5_filenames = [
chunk_out.out_molecules for chunk_out in chunk_outs
]
cr_mol_counter.MoleculeCounter.concatenate(outs.out_molecules,
input_h5_filenames)
else:
# just copy input molecules
cr_utils.copy(args.molecules, outs.out_molecules)
# merge summaries
summary = merge_summaries(chunk_outs)
summary['downsample_info'] = downsample_map
with open(outs.summary, 'w') as f:
json.dump(summary, f, indent=4, sort_keys=True)
def join(args, outs, chunk_defs, chunk_outs):
chunk_out = chunk_outs[0]
cr_utils.copy(chunk_out.summary, outs.summary)
cr_utils.copy(chunk_out.filtered_matrices_h5, outs.filtered_matrices_h5)
cr_utils.copy(chunk_out.filtered_barcodes, outs.filtered_barcodes)
cr_utils.copytree(chunk_out.filtered_matrices_mex,
outs.filtered_matrices_mex)
def join(args, outs, chunk_defs, chunk_outs):
summary_files = [
args.extract_reads_summary,
args.correct_barcodes_summary,
]
summary_files = [sum_file for sum_file in summary_files if not sum_file is None]
cr_report.merge_jsons(summary_files, outs.summary)
cr_utils.copy(args.raw_barcode_counts, outs.raw_barcode_counts)
cr_utils.copy(args.corrected_barcode_counts, outs.corrected_barcode_counts)
cr_utils.copy(args.barcode_summary, outs.barcode_summary)
outs.gem_groups = args.gem_groups
outs.read_groups = args.read_groups
outs.align = args.align
outs.bam_comments = args.bam_comments
outs.bc_corrected_read1s = [out.bc_corrected_read1s for out in chunk_outs]
outs.bc_corrected_read2s = [out.bc_corrected_read2s for out in chunk_outs]
def main(args, outs):
if args.read1s is not None:
cr_utils.copy(args.read1s, outs.bc_corrected_read1s)
if args.read2s is not None:
cr_utils.copy(args.read2s, outs.bc_corrected_read2s)
def join(args, outs, chunk_defs, chunk_outs):
outs.chain_type = chunk_outs[0].chain_type
cr_utils.copy(chunk_outs[0].summary, outs.summary)
def main(args, outs):
reporter = vdj_report.VdjReporter(
vdj_reference_path=args.vdj_reference_path)
gene_umi_counts_per_bc = {}
strand = cr_chem.get_strandedness(args.chemistry_def)
paired_end = cr_chem.is_paired_end(args.chemistry_def)
assert paired_end != (args.read2_chunk is None)
# For the entire chunk, match reads against the V(D)J reference
ref_fasta = vdj_reference.get_vdj_reference_fasta(args.vdj_reference_path)
# The filtering code will write this bam. Then we'll read it, correct the UMIs
# and write outs.chunked_bams.
filter_bam = martian.make_path('tmp.bam')
vdj_filt.run_read_match(args.read1_chunk, args.read2_chunk, ref_fasta,
filter_bam, strand, args.sw_params)
# Make two passes over the BAM file, processing one barcode at a time
bam1 = pysam.AlignmentFile(filter_bam, check_sq=False)
bam2 = pysam.AlignmentFile(filter_bam, check_sq=False)
bc_iter1 = get_bc_grouped_pair_iter(bam1, paired_end)
bc_iter2 = get_bc_grouped_pair_iter(bam2, paired_end)
reads_per_bc = open(outs.reads_per_bc, 'w')
out_bam, _ = tk_bam.create_bam_outfile(outs.barcode_chunked_bams,
None,
None,
template=bam1)
for (bc, pair_iter1), (_,
pair_iter2) in itertools.izip(bc_iter1, bc_iter2):
nreads = 0
# Pass 1: UMI correction
umi_counts = defaultdict(int)
for header, (read1, read2) in pair_iter1:
nreads += 2
umi_counts[header.get_tag(cr_constants.RAW_UMI_TAG)] += 1
corrected_umis = correct_umis(umi_counts)
# Pass 2: Write the UMI-corrected records
process_bam_barcode(bam1, pair_iter2, bc, corrected_umis, reporter,
gene_umi_counts_per_bc, strand, out_bam,
paired_end)
reads_per_bc.write('{}\t{}\n'.format(bc, nreads))
bam1.close()
bam2.close()
out_bam.close()
# Write bc-gene-umi counts
cPickle.dump(gene_umi_counts_per_bc, open(outs.chunked_gene_umi_counts,
'w'))
# Copy the input barcodes
if args.barcodes_chunk is not None:
cr_utils.copy(args.barcodes_chunk, outs.barcodes_in_chunks)
else:
outs.barcodes_in_chunks = None
reporter.save(outs.chunked_reporter)
def join(args, outs, chunk_defs, chunk_outs):
contigs = []
contig_fastqs = []
contig_bams = []
if len(chunk_outs) == 0:
# No input reads
# Create empty BAM file
with open(outs.contig_bam, 'w') as f:
pass
outs.contig_bam_bai = None
# Create empty contig FASTA
with open(outs.contig_fasta, 'w') as f:
pass
outs.contig_fasta_fai = None
# Create empty contig FASTQ
with open(outs.contig_fastq, 'w') as f:
pass
outs.metrics_summary_json = None
outs.summary_tsv = None
outs.umi_summary_tsv = None
return
summary_tsvs = []
umi_summary_tsvs = []
for chunk_out in chunk_outs:
if not os.path.isfile(chunk_out.contig_fasta):
continue
contigs.append(chunk_out.contig_fasta)
contig_fastqs.append(chunk_out.contig_fastq)
contig_bams.append(chunk_out.contig_bam)
summary_tsvs.append(chunk_out.summary_tsv)
umi_summary_tsvs.append(chunk_out.umi_summary_tsv)
cr_utils.concatenate_files(outs.contig_fasta, contigs)
if os.path.getsize(outs.contig_fasta) > 0:
tk_subproc.check_call('samtools faidx %s' % outs.contig_fasta,
shell=True)
outs.contig_fasta_fai = outs.contig_fasta + '.fai'
cr_utils.concatenate_files(outs.contig_fastq, contig_fastqs)
if len(summary_tsvs) > 0:
cr_utils.concatenate_headered_files(outs.summary_tsv, summary_tsvs)
if len(umi_summary_tsvs) > 0:
cr_utils.concatenate_headered_files(outs.umi_summary_tsv,
umi_summary_tsvs)
if contig_bams:
# Merge every N BAMs. Trying to merge them all at once
# risks hitting the filehandle limit.
n_merged = 0
while len(contig_bams) > 1:
to_merge = contig_bams[0:MERGE_BAMS_N]
tmp_bam = martian.make_path('merged-%04d.bam' % n_merged)
n_merged += 1
print "Merging %d BAMs into %s ..." % (len(to_merge), tmp_bam)
tk_bam.merge(tmp_bam, to_merge, threads=args.__threads)
# Delete any temporary bams that have been merged
for in_bam in to_merge:
if os.path.basename(in_bam).startswith('merged-'):
cr_utils.remove(in_bam)
# Pop the input bams and push the merged bam
contig_bams = contig_bams[len(to_merge):] + [tmp_bam]
if os.path.basename(contig_bams[0]).startswith('merged-'):
# We merged at least two chunks together.
# Rename it to the output bam.
cr_utils.move(contig_bams[0], outs.contig_bam)
else:
# There was only a single chunk, so copy it from the input
cr_utils.copy(contig_bams[0], outs.contig_bam)
tk_bam.index(outs.contig_bam)
# Make sure the Martian out matches the actual index filename
outs.contig_bam_bai = outs.contig_bam + '.bai'
# Merge the assembler summary jsons
merged_summary = cr_utils.merge_jsons_single_level(
[out.metrics_summary_json for out in chunk_outs])
with open(outs.metrics_summary_json, 'w') as f:
json.dump(tk_safe_json.json_sanitize(merged_summary),
f,
indent=4,
sort_keys=True)
def join(args, outs, chunk_defs, chunk_outs):
cr_utils.copy(chunk_outs[0].summary, outs.summary)
def build_reference_fasta_from_ensembl(gtf_paths, transcripts_to_remove_path,
genome_fasta_path, reference_path,
reference_name, ref_version,
mkref_version):
"""Create cellranger-compatible vdj reference files from a list of ENSEMBL-like GTF files.
Input files are concatenated. No attempt to merge/reconcile information
across them is made. Providing the files in a different order might change the
output in cases where there are multiple entries with the same transcript id
and the same feature type (eg. V-region).
"""
transcripts = collections.defaultdict(list)
if transcripts_to_remove_path:
with open(transcripts_to_remove_path) as f:
rm_transcripts = set([line.strip() for line in f.readlines()])
else:
rm_transcripts = set()
# Note: We cannot symlink here because some filesystems in the wild
# do not support symlinks.
print 'Copying genome reference sequence...'
os.makedirs(os.path.dirname(get_vdj_reference_fasta(reference_path)))
tmp_genome_fa_path = os.path.join(reference_path, 'genome.fasta')
cr_utils.copy(genome_fasta_path, tmp_genome_fa_path)
print '...done.\n'
print 'Indexing genome reference sequence...'
tk_subproc.check_call(['samtools', 'faidx', tmp_genome_fa_path])
print '...done.\n'
print 'Loading genome reference sequence...'
genome_fasta = pysam.FastaFile(tmp_genome_fa_path)
print '...done.\n'
print 'Computing hash of genome FASTA file...'
fasta_hash = cr_utils.compute_hash_of_file(tmp_genome_fa_path)
print '...done.\n'
for gtf in gtf_paths:
print 'Reading GTF {}'.format(gtf)
for line_no, entry in enumerate(get_gtf_iter(open(gtf))):
if not entry.feature in [
ENSEMBL_FIVE_PRIME_UTR_FEATURE, ENSEMBL_CDS_FEATURE
]:
continue
entry = parse_attributes(entry)
transcript_id = entry.attributes.get('transcript_id')
transcript_biotype = entry.attributes.get('transcript_biotype')
gene_biotype = entry.attributes.get('gene_biotype')
gene_name = entry.attributes.get('gene_name')
# Skip irrelevant biotypes
if transcript_biotype not in ENSEMBL_VDJ_BIOTYPES and not gene_biotype in ENSEMBL_VDJ_BIOTYPES:
continue
# Skip blacklisted gene names
if transcript_id in rm_transcripts:
continue
# Warn and skip if transcript_id missing
if transcript_id is None:
print 'Warning: Entry on row %d has no transcript_id' % line_no
continue
# Warn and skip if gene_name missing
if gene_name is None:
print 'Warning: Transcript %s on row %d has biotype %s but no gene_name. Skipping.' % (
transcript_id, line_no, transcript_biotype)
continue
# Infer region type from biotype
if transcript_biotype in ENSEMBL_VDJ_BIOTYPES:
vdj_feature = infer_ensembl_vdj_feature_type(
entry.feature, transcript_biotype)
else:
vdj_feature = infer_ensembl_vdj_feature_type(
entry.feature, gene_biotype)
# Warn and skip if region type could not be inferred
if vdj_feature is None:
print 'Warning: Transcript %s has biotype %s. Could not infer VDJ gene type. Skipping.' % (
transcript_id, transcript_biotype)
continue
# Features that share a transcript_id and feature type are presumably exons
# so keep them together.
transcripts[(transcript_id, vdj_feature)].append(entry)
print '...done.\n'
print 'Computing hash of genes GTF files...'
digest = hashlib.sha1()
# concatenate all the hashes into a string and then hash that string
digest.update(
reduce(lambda x, y: x + y,
[cr_utils.compute_hash_of_file(gtf) for gtf in gtf_paths]))
gtf_hash = digest.hexdigest()
print '...done.\n'
print 'Fetching sequences...'
out_fasta = open(get_vdj_reference_fasta(reference_path), 'w')
feature_id = 1
seen_features = set()
for (transcript_id, region_type), regions in transcripts.iteritems():
if not all(r.chrom == regions[0].chrom for r in regions):
chroms = sorted(list(set([r.chrom for r in regions])))
print 'Warning: Transcript %s spans multiple contigs: %s. Skipping.' % (
transcript_id, str(chroms))
continue
if not all(r.strand == regions[0].strand for r in regions):
print 'Warning: Transcript %s spans multiple strands. Skipping.' % transcript_id
continue
chrom = regions[0].chrom
strand = regions[0].strand
ens_gene_name = standardize_ensembl_gene_name(
regions[0].attributes['gene_name'])
transcript_id = regions[0].attributes['transcript_id']
if chrom not in genome_fasta:
print 'Warning: Transcript %s is on contig "%s" which is not in the provided reference fasta. Skipping.' % (
transcript_id, chrom)
continue
# Build sequence
regions.sort(key=lambda r: r.start)
seq = ''
for region in regions:
# GTF coordinates are 1-based
start, end = int(region.start) - 1, int(region.end)
seq += genome_fasta.fetch(chrom, start, end)
# Revcomp if transcript on reverse strand
if strand == '-':
seq = tk_seq.get_rev_comp(seq)
# Strip Ns from termini
if 'N' in seq:
print 'Warning: Feature %s contains Ns. Stripping from the ends.' % str(
(ens_gene_name, transcript_id, region_type))
seq = seq.strip('N')
if len(seq) == 0:
print 'Warning: Feature %s is all Ns. Skipping.' % str(
(ens_gene_name, transcript_id, region_type))
continue
# Infer various attributes from the Ensembl gene name
record_id = transcript_id
gene_name = ens_gene_name
display_name = make_display_name(gene_name=gene_name, allele_name=None)
chain = infer_ensembl_vdj_chain(gene_name)
chain_type = infer_ensembl_vdj_chain_type(gene_name)
# Ensembl doesn't encode alleles
allele_name = '00'
# Disallow spaces in these fields
if ' ' in region_type:
raise ValueError('Spaces not allowed in region type: "%s"' %
region_type)
if ' ' in gene_name:
raise ValueError('Spaces not allowed in gene name: "%s"' %
gene_name)
if ' ' in record_id:
raise ValueError('Spaces not allowed in record ID: "%s"' %
record_id)
# Warn on features we couldn't classify properly
if chain_type not in vdj_constants.VDJ_CHAIN_TYPES:
print ('Warning: Could not infer chain type for: %s. ' + \
'Expected the first two characters of the gene name to be in %s. Feature skipped.') % \
(str((gene_name, record_id, region_type)),
str(tuple(vdj_constants.VDJ_CHAIN_TYPES)))
continue
if region_type in vdj_constants.VDJ_C_FEATURE_TYPES and chain in vdj_constants.CHAINS_WITH_ISOTYPES:
isotype = infer_ensembl_isotype(ens_gene_name)
else:
isotype = None
feature = VdjAnnotationFeature(
feature_id=feature_id,
record_id=record_id,
display_name=display_name,
gene_name=gene_name,
region_type=region_type,
chain_type=chain_type,
chain=chain,
isotype=isotype,
allele_name=allele_name,
sequence=seq,
)
# Don't add duplicate entries
feat_key = get_duplicate_feature_key(feature)
if feat_key in seen_features:
print 'Warning: Skipping duplicate entry for %s (%s, %s).' % (
display_name, region_type, record_id)
continue
seen_features.add(feat_key)
feature_id += 1
out_fasta.write(convert_vdj_feature_to_fasta_entry(feature) + '\n')
print '...done.\n'
print 'Deleting copy of genome fasta...'
os.remove(tmp_genome_fa_path)
os.remove(tmp_genome_fa_path + '.fai')
print '...done.\n'
print 'Writing metadata JSON file into reference folder...'
metadata = {
cr_constants.REFERENCE_GENOMES_KEY:
reference_name,
cr_constants.REFERENCE_FASTA_HASH_KEY:
fasta_hash,
cr_constants.REFERENCE_GTF_HASH_KEY:
gtf_hash,
cr_constants.REFERENCE_INPUT_FASTA_KEY:
os.path.basename(genome_fasta_path),
cr_constants.REFERENCE_INPUT_GTF_KEY:
','.join([os.path.basename(gtf_path) for gtf_path in gtf_paths]),
cr_constants.REFERENCE_VERSION_KEY:
ref_version,
cr_constants.REFERENCE_MKREF_VERSION_KEY:
mkref_version,
cr_constants.REFERENCE_TYPE_KEY:
vdj_constants.REFERENCE_TYPE,
}
with open(
os.path.join(reference_path, cr_constants.REFERENCE_METADATA_FILE),
'w') as json_file:
json.dump(tk_safe_json.json_sanitize(metadata),
json_file,
sort_keys=True,
indent=4)
print '...done.\n'
def main(args, outs):
if args.summary is not None:
cr_utils.copy(args.summary, outs.summary)
if args.barcodes_detected is not None:
cr_utils.copy(args.barcodes_detected, outs.barcodes_detected)
def join(args, outs, chunk_defs, chunk_outs):
if chunk_outs[0].output_for_cloupe is None:
# Set output to null if noloupe is set, or if we ran on a barnyard
outs.output_for_cloupe = None
else:
cr_utils.copy(chunk_outs[0].output_for_cloupe, outs.output_for_cloupe)
def join(args, outs, chunk_defs, chunk_outs):
cr_utils.copy(chunk_outs[0].summary, outs.summary)
if chunk_outs[0].report is not None:
cr_utils.copy(chunk_outs[0].report, outs.report)
outs.chemistry_type = chunk_outs[0].chemistry_type
def main(args, outs):
cr_utils.copy(args.trim_reads_summary, outs.summary)
def join(args, outs, chunk_defs, chunk_outs):
chunk_out = chunk_outs[0]
cr_utils.copy(chunk_out.web_summary, outs.web_summary)
cr_utils.copy(chunk_out.summary, outs.summary)
def join(args, outs, chunk_defs, chunk_outs):
cr_utils.copy(chunk_outs[0].cell_barcodes, outs.cell_barcodes)
cr_utils.copy(chunk_outs[0].barcode_support, outs.barcode_support)
cr_utils.copy(chunk_outs[0].summary, outs.summary)
cr_utils.copy(chunk_outs[0].barcode_umi_summary, outs.barcode_umi_summary)
def join(args, outs, chunk_defs, chunk_outs):
outs.min_readpairs_per_umi = chunk_outs[0].min_readpairs_per_umi
cr_utils.copy(chunk_outs[0].cell_barcodes, outs.cell_barcodes)
cr_utils.copy(chunk_outs[0].barcode_support, outs.barcode_support)
cr_utils.copy(chunk_outs[0].summary, outs.summary)
cr_utils.copy(chunk_outs[0].barcode_umi_summary, outs.barcode_umi_summary)
