def main(args, outs):
summary_files = [
args.cluster_summary,
args.evaluate_summary,
]
cr_report.merge_jsons(summary_files, outs.summary)
def main(args, outs):
cr_report.merge_jsons(args.summaries, outs.metrics_summary_json)
sample_data_paths = cr_webshim_data.SampleDataPaths(
summary_path=outs.metrics_summary_json,
barcode_summary_path=args.barcode_summary_h5,
analysis_path=args.analysis,
filtered_barcodes_path=args.filtered_barcodes,
)
genomes = cr_utils.get_reference_genomes(args.reference_path)
sample_properties = CountSampleProperties(
sample_id=args.sample_id,
sample_desc=args.sample_desc,
genomes=genomes,
version=martian.get_pipelines_version())
sample_properties = dict(sample_properties._asdict())
sample_data = cr_webshim.load_sample_data(sample_properties,
sample_data_paths)
cr_webshim.build_web_summary_html(outs.web_summary,
sample_properties,
sample_data,
PIPELINE_COUNT,
alerts_output_filename=outs.alerts)
cr_webshim.build_metrics_summary_csv(outs.metrics_summary_csv,
sample_properties, sample_data,
PIPELINE_COUNT)
def main(args, outs):
summary_files = [
args.extract_reads_summary,
args.attach_bcs_and_umis_summary,
args.mark_duplicates_summary,
args.count_genes_reporter_summary,
args.filter_barcodes_summary,
args.subsample_molecules_summary,
]
cr_report.merge_jsons(summary_files, outs.summary,
[cr_utils.build_alignment_param_metrics(args.align)])
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):
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]
