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Snakefile
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Snakefile
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import itertools
import sys
import re
import json
import traceback
import pathlib
import parse
from urllib.parse import urlparse
import datetime
###############################
###### Preprocess Config ######
###############################
print("Preprocessing config", flush = True)
configfile: "config/default.yml"
# Allow to configure to use conda from the config file
if 'use_conda' in config and config['use_conda']:
workflow.use_conda = True
workflow.global_resources["contigvalidator"] = 1
DATADIR = "data"
if "datadir" in config:
DATADIR = config["datadir"]
print("DATADIR: {}".format(DATADIR))
MAX_THREADS = 56
print(f"Setting MAX_THREADS to {MAX_THREADS}", flush = True)
BUILD_THREADS = 7
print(f"Setting BUILD_THREADS to {BUILD_THREADS}", flush = True)
# Preprocess experiments configuration
genomes = config["genomes"]
corrected_genomes = config["corrected_genomes"]
reports = config["reports"]
aggregated_reports = config["aggregated_reports"]
if aggregated_reports is None:
aggregated_reports = {}
from report_file_parser import *
DEFAULT_ASSEMBLER_ARGUMENTS = {
"wtdbg2": {
"skip_fragment_assembly": "no",
"fragment_correction_steps": "all",
"tig_injection": "none",
"frg_injection": "none",
"frg_injection_stage": "none",
"hodeco_consensus": "none",
},
"mdbg": {
"mdbg_mode": "multik",
},
"hifiasm": {
"contig_algorithm": "builtin",
},
}
for report_name, report_definition in reports.items():
argument_matrix = ArgumentMatrix(report_definition.setdefault("argument_matrix", {}))
report_definition["argument_matrix"] = argument_matrix # use correct type
# print("Matrix of {} has length {}".format(report_name, len(argument_matrix)))
# entries = list(iter(argument_matrix))
# print("Entries in matrix:")
# for entry in entries:
# print(entry)
for arguments in argument_matrix:
genome_arguments = Arguments.from_dict(genomes[arguments["genome"]].setdefault("genome_arguments", {}))
genome_arguments.update(arguments)
arguments = genome_arguments # update method works in-place
arguments.setdefault("read_source", "real")
arguments.setdefault("read_simulation_model_source", "none")
arguments.setdefault("read_downsampling_factor", "none")
arguments.setdefault("homopolymer_compression", "none")
arguments.setdefault("uniquify_ids", "no")
arguments.setdefault("assembler", None)
arguments.setdefault("assembler_arguments", None)
arguments.setdefault("quast_mode", "normal")
arguments.setdefault("filter_nw", "no")
arguments.setdefault("retain_cm", "no")
arguments.setdefault("filter_plasmids", "no")
# hisim produces reads with duplicate ids, so we always need to uniquify those
if arguments["read_source"].startswith("hisim_"):
arguments["uniquify_ids"] = "yes"
columns = []
for column_definition in report_definition["columns"]:
column_arguments = Arguments.from_dict(column_definition)
column = Column(arguments, column_arguments)
assembler_name = column.arguments.assembler_name()
if assembler_name in DEFAULT_ASSEMBLER_ARGUMENTS:
#print(f"assembler_name: {assembler_name}")
assembler_arguments = column.arguments.assembler_arguments()
#print(f"assembler_arguments: {assembler_arguments}")
for key, value in DEFAULT_ASSEMBLER_ARGUMENTS[assembler_name].items():
assembler_arguments.setdefault(key, value)
#print(f"assembler_arguments: {assembler_arguments}")
#print(column, flush = True)
columns.append(column)
report_file = ReportFile(arguments, columns)
report_definition.setdefault("report_files", {})[report_file.name] = report_file
#import pprint
#pp = pprint.PrettyPrinter(indent = 2, width = 200, compact = True)
#pp.pprint(reports)
#pp.pprint(aggregated_reports)
#print("Exiting for debugging")
#sys.exit(0)
# Collect all rust sources
RUST_SOURCES = list(map(str, itertools.chain(pathlib.Path('implementation').glob('**/Cargo.toml'), pathlib.Path('implementation').glob('**/*.rs'))))
import datetime
today = datetime.date.today().isoformat()
print("Finished config preprocessing", flush = True)
#########################
###### Directories ######
#########################
EXTERNAL_SOFTWARE_ROOTDIR = os.path.join(DATADIR, "external-software")
DOWNLOAD_ROOTDIR = os.path.join(DATADIR, "downloads")
GENOME_ROOTDIR = os.path.join(DATADIR, "genomes")
SIMULATION_ROOTDIR = os.path.join(DATADIR, "simulation")
ASSEMBLY_ROOTDIR = os.path.join(DATADIR, "assembly")
EVALUATION_ROOTDIR = os.path.join(DATADIR, "evaluation")
REPORT_ROOTDIR = os.path.join(DATADIR, "reports")
# Genomes
GENOME_ARGUMENT_STRING = "g{genome}-h{homopolymer_compression}"
GENOME_REFERENCE_ARGUMENT_STRING = "reference-n{filter_nw}-c{retain_cm}-p{filter_plasmids}"
GENOME_REFERENCE_SUBDIR = os.path.join(GENOME_ARGUMENT_STRING, GENOME_REFERENCE_ARGUMENT_STRING)
GENOME_REFERENCE = os.path.join(GENOME_ROOTDIR, GENOME_REFERENCE_SUBDIR, "reference.fa")
GENOME_REFERENCE_LENGTH = os.path.join(GENOME_ROOTDIR, GENOME_REFERENCE_SUBDIR, "reference_length.txt")
GENOME_READS_ARGUMENT_STRING = "reads-s{read_source}-m{read_simulation_model_source}-r{read_downsampling_factor}-u{uniquify_ids}"
GENOME_READS_SUBDIR = os.path.join(GENOME_ARGUMENT_STRING, GENOME_READS_ARGUMENT_STRING)
GENOME_READS_DIR = os.path.join(GENOME_ROOTDIR, GENOME_READS_SUBDIR)
GENOME_READS = os.path.join(GENOME_READS_DIR, "reads.fa")
GENOME_SINGLE_LINE_READS = os.path.join(GENOME_ROOTDIR, GENOME_READS_SUBDIR, "single_line_reads.fa")
UNIQUIFY_IDS_LOG = os.path.join(GENOME_ROOTDIR, GENOME_READS_SUBDIR, "uniquify_ids.log")
HOCO_READS_LOG = os.path.join(GENOME_ROOTDIR, GENOME_READS_SUBDIR, "hoco.log")
HOCO_REFERENCE_LOG = os.path.join(GENOME_ROOTDIR, GENOME_REFERENCE_SUBDIR, "hoco.log")
# Simulations
FASTK_ARGUMENT_STRING = "k{fastk_k}"
FASTK_OUTPUT_DIR = os.path.join(SIMULATION_ROOTDIR, "fastk", GENOME_READS_SUBDIR, FASTK_ARGUMENT_STRING)
FASTK_INPUT_READS = os.path.join(FASTK_OUTPUT_DIR, "reads.fa")
FASTK_TABLE = os.path.join(FASTK_OUTPUT_DIR, "reads.ktab")
FASTK_PROFILE = os.path.join(FASTK_OUTPUT_DIR, "reads.prof")
FASTK_HIST = os.path.join(FASTK_OUTPUT_DIR, "reads.hist")
FASTK_SYMMETRIC_TABLE = os.path.join(FASTK_OUTPUT_DIR, "symmetric_reads", "symmetric_reads.ktab")
FASTK_HISTEX_EVALUATION = os.path.join(EVALUATION_ROOTDIR, "histex", GENOME_READS_SUBDIR, FASTK_ARGUMENT_STRING, "histogram.txt")
HISIM_ARGUMENT_STRING = "a{himodel_kmer_threshold}-l{himodel_min_valid}-h{himodel_max_valid}"
HIMODEL_OUTPUT_DIR = os.path.join(SIMULATION_ROOTDIR, "himodel", GENOME_READS_SUBDIR, FASTK_ARGUMENT_STRING, HISIM_ARGUMENT_STRING)
HIMODEL_INPUT_SYMMETRIC_TABLE = os.path.join(HIMODEL_OUTPUT_DIR, "reads.ktab")
HIMODEL_INPUT_PROFILE = os.path.join(HIMODEL_OUTPUT_DIR, "reads.prof")
HIMODEL_MODEL = os.path.join(HIMODEL_OUTPUT_DIR, "reads.model")
HISIM_HAPLOTYPE = os.path.join(GENOME_READS_DIR, "reads.hap{haplotype_index}.fasta")
# Assemblies
ASSEMBLY_ARGUMENT_STRING = "a{assembler}--{assembler_arguments}-"
ASSEMBLY_SUBDIR = os.path.join(GENOME_READS_SUBDIR, ASSEMBLY_ARGUMENT_STRING)
ASSEMBLY_OUTPUT_DIR = os.path.join(ASSEMBLY_ROOTDIR, ASSEMBLY_SUBDIR)
ASSEMBLED_CONTIGS = os.path.join(ASSEMBLY_OUTPUT_DIR, "contigs.fa")
ASSEMBLY_LOG = os.path.join(ASSEMBLY_OUTPUT_DIR, "assembly.log")
ASSEMBLER_ARGUMENT_STRINGS = {}
WTDBG2_ARGUMENT_STRING = "m{wtdbg2_mode}-s{skip_fragment_assembly}-f{fragment_correction_steps}-t{tig_injection}-f{frg_injection}-s{frg_injection_stage}-d{hodeco_consensus}-c{retain_cm}"
ASSEMBLER_ARGUMENT_STRINGS["wtdbg2"] = WTDBG2_ARGUMENT_STRING
WTDBG2_SUBDIR = safe_format(ASSEMBLY_SUBDIR, assembler = "wtdbg2", assembler_arguments = WTDBG2_ARGUMENT_STRING)
WTDBG2_OUTPUT_DIR = os.path.join(ASSEMBLY_ROOTDIR, WTDBG2_SUBDIR)
WTDBG2_INJECTABLE_CONTIG_DIR = os.path.join(WTDBG2_OUTPUT_DIR, "injectable_contigs")
WTDBG2_INJECTABLE_FRAGMENT_CONTIG_DIR = os.path.join(WTDBG2_OUTPUT_DIR, "injectable_fragment_contigs")
WTDBG2_OUTPUT_DIR_PACKED = safe_format(os.path.join(ASSEMBLY_ROOTDIR, ASSEMBLY_SUBDIR), assembler = "wtdbg2")
WTDBG2_LOG = os.path.join(WTDBG2_OUTPUT_DIR, "assembly.log")
WTDBG2_EXTRACT_LOG = os.path.join(WTDBG2_OUTPUT_DIR, "extract.{subfile}.log")
WTDBG2_CONSENSUS_LOG = os.path.join(WTDBG2_OUTPUT_DIR, "wtdbg2_consensus.log")
WTDBG2_ASSEMBLED_CONTIGS = os.path.join(WTDBG2_OUTPUT_DIR, "contigs.fa")
FLYE_ARGUMENT_STRING = "m{flye_mode}-c{retain_cm}"
ASSEMBLER_ARGUMENT_STRINGS["flye"] = FLYE_ARGUMENT_STRING
FLYE_SUBDIR = safe_format(ASSEMBLY_SUBDIR, assembler = "flye", assembler_arguments = FLYE_ARGUMENT_STRING)
FLYE_OUTPUT_DIR = os.path.join(ASSEMBLY_ROOTDIR, FLYE_SUBDIR)
FLYE_OUTPUT_DIR_PACKED = safe_format(os.path.join(ASSEMBLY_ROOTDIR, ASSEMBLY_SUBDIR), assembler = "flye")
FLYE_LOG = os.path.join(FLYE_OUTPUT_DIR, "assembly.log")
FLYE_ASSEMBLED_CONTIGS = os.path.join(FLYE_OUTPUT_DIR, "contigs.fa")
HIFIASM_ARGUMENT_STRING = "c{contig_algorithm}"
ASSEMBLER_ARGUMENT_STRINGS["hifiasm"] = HIFIASM_ARGUMENT_STRING
HIFIASM_SUBDIR = safe_format(ASSEMBLY_SUBDIR, assembler = "hifiasm", assembler_arguments = HIFIASM_ARGUMENT_STRING)
HIFIASM_OUTPUT_DIR = os.path.join(ASSEMBLY_ROOTDIR, HIFIASM_SUBDIR)
HIFIASM_OUTPUT_DIR_PACKED = safe_format(os.path.join(ASSEMBLY_ROOTDIR, ASSEMBLY_SUBDIR), assembler = "hifiasm")
HIFIASM_LOG = os.path.join(HIFIASM_OUTPUT_DIR, "assembly.log")
HIFIASM_ASSEMBLED_CONTIGS = os.path.join(HIFIASM_OUTPUT_DIR, "contigs.fa")
MDBG_ARGUMENT_STRING = "m{mdbg_mode}"
ASSEMBLER_ARGUMENT_STRINGS["mdbg"] = MDBG_ARGUMENT_STRING
MDBG_SUBDIR = safe_format(ASSEMBLY_SUBDIR, assembler = "mdbg", assembler_arguments = MDBG_ARGUMENT_STRING)
MDBG_OUTPUT_DIR = os.path.join(ASSEMBLY_ROOTDIR, MDBG_SUBDIR)
MDBG_OUTPUT_DIR_PACKED = safe_format(os.path.join(ASSEMBLY_ROOTDIR, ASSEMBLY_SUBDIR), assembler = "mdbg")
MDBG_LOG = os.path.join(MDBG_OUTPUT_DIR, "assembly.log")
MDBG_ASSEMBLED_CONTIGS = os.path.join(MDBG_OUTPUT_DIR, "contigs.fa")
LJA_ARGUMENT_STRING = "none"
ASSEMBLER_ARGUMENT_STRINGS["lja"] = LJA_ARGUMENT_STRING
LJA_SUBDIR = safe_format(ASSEMBLY_SUBDIR, assembler = "lja", assembler_arguments = LJA_ARGUMENT_STRING)
LJA_OUTPUT_DIR = os.path.join(ASSEMBLY_ROOTDIR, LJA_SUBDIR)
LJA_OUTPUT_DIR_PACKED = safe_format(os.path.join(ASSEMBLY_ROOTDIR, ASSEMBLY_SUBDIR), assembler = "lja")
LJA_LOG = os.path.join(LJA_OUTPUT_DIR, "assembly.log")
LJA_ASSEMBLED_CONTIGS = os.path.join(LJA_OUTPUT_DIR, "contigs.fa")
CANU_ARGUMENT_STRING = "c{retain_cm}"
ASSEMBLER_ARGUMENT_STRINGS["canu"] = CANU_ARGUMENT_STRING
CANU_SUBDIR = safe_format(ASSEMBLY_SUBDIR, assembler = "canu", assembler_arguments = CANU_ARGUMENT_STRING)
CANU_OUTPUT_DIR = os.path.join(ASSEMBLY_ROOTDIR, CANU_SUBDIR)
CANU_OUTPUT_DIR_PACKED = safe_format(os.path.join(ASSEMBLY_ROOTDIR, ASSEMBLY_SUBDIR), assembler = "canu")
CANU_LOG = os.path.join(CANU_OUTPUT_DIR, "assembly.log")
CANU_ASSEMBLED_CONTIGS = os.path.join(CANU_OUTPUT_DIR, "contigs.fa")
# Evaluations
QUAST_ROOTDIR = os.path.join(EVALUATION_ROOTDIR, "quast-m{quast_mode}")
QUAST_SUBDIR = os.path.join(GENOME_ARGUMENT_STRING, GENOME_REFERENCE_ARGUMENT_STRING, GENOME_READS_ARGUMENT_STRING, ASSEMBLY_ARGUMENT_STRING)
QUAST_OUTPUT_DIR = os.path.join(QUAST_ROOTDIR, QUAST_SUBDIR)
RESOURCES_ROOTDIR = os.path.join(EVALUATION_ROOTDIR, "resources")
RESOURCES_SUBDIR = os.path.join(GENOME_ARGUMENT_STRING, GENOME_REFERENCE_ARGUMENT_STRING, GENOME_READS_ARGUMENT_STRING, ASSEMBLY_ARGUMENT_STRING)
RESOURCES_OUTPUT_DIR = os.path.join(RESOURCES_ROOTDIR, RESOURCES_SUBDIR)
RESOURCES_EVALUATION = os.path.join(RESOURCES_OUTPUT_DIR, "resources.json")
# Reports
REPORT_SUBDIR = os.path.join(REPORT_ROOTDIR, "{report_name}", "{report_file_name}")
REPORT_TEX = os.path.join(REPORT_SUBDIR, "report.tex")
REPORT_COMBINED_EAXMAX_PLOT = os.path.join(REPORT_SUBDIR, "combined_eaxmax_plot.pdf")
REPORT_NAME_FILE = os.path.join(REPORT_SUBDIR, "name.txt")
REPORT_HASHDIR = os.path.join(REPORT_ROOTDIR, "hashdir")
REPORT_PDF = os.path.join(REPORT_SUBDIR, "report.pdf")
AGGREGATED_REPORT_SUBDIR = os.path.join(REPORT_ROOTDIR, "{aggregated_report_name}")
AGGREGATED_REPORT_PDF = os.path.join(AGGREGATED_REPORT_SUBDIR, "aggregated_report.pdf")
UNIQUIFY_IDS_SCRIPT = "scripts/uniquify_fasta_ids.py"
CONVERT_VALIDATION_OUTPUTS_TO_LATEX_SCRIPT = "scripts/convert_validation_outputs_to_latex.py"
CREATE_AGGREGATED_WTDBG2_REPORT_SCRIPT = "scripts/create_aggregated_wtdbg2_report.py"
CREATE_COMBINED_EAXMAX_PLOT_SCRIPT = "scripts/create_combined_eaxmax_plot.py"
DOWNSAMPLE_FASTA_READS_SCRIPT = "scripts/downsample_fasta_reads.py"
FILTER_NW_FROM_REFERENCE_SCRIPT = "scripts/filter_nw_from_reference.py"
RETAIN_CM_IN_REFERENCE_SCRIPT = "scripts/retain_cm_in_reference.py"
FILTER_PLASMIDS_IN_REFERENCE_SCRIPT = "scripts/filter_plasmids_in_reference.py"
COMPUTE_GENOME_REFERENCE_LENGTH_SCRIPT = "scripts/compute_genome_reference_length.py"
WTDBG2_HODECO_SCRIPT = "scripts/wtdbg2_hodeco.py"
EXTERNAL_SOFTWARE_SCRIPTS_DIR = os.path.join(EXTERNAL_SOFTWARE_ROOTDIR, "scripts")
RUST_DIR = os.path.join(EXTERNAL_SOFTWARE_ROOTDIR, "rust_target")
IS_RUST_TESTED_MARKER = os.path.join(RUST_DIR, "is_rust_tested.marker")
IS_RUST_FETCHED_MARKER = os.path.join(RUST_DIR, "is_rust_fetched.marker")
RUST_BINARY = os.path.join(RUST_DIR, "release", "cli")
QUAST_BINARY = os.path.join(EXTERNAL_SOFTWARE_ROOTDIR, "quast", "quast.py")
WTDBG2_DIR = os.path.join(EXTERNAL_SOFTWARE_ROOTDIR, "wtdbg2")
WTDBG2_BINARY = os.path.join(WTDBG2_DIR, "wtdbg2")
WTDBG2_CONSENSUS_BINARY = os.path.join(WTDBG2_DIR, "wtpoa-cns")
FLYE_DIR = os.path.join(EXTERNAL_SOFTWARE_ROOTDIR, "Flye")
FLYE_BINARY = os.path.join(FLYE_DIR, "bin", "flye")
SIM_IT_BINARY = os.path.join(EXTERNAL_SOFTWARE_ROOTDIR, "sim-it", "sim-it.pl")
RATATOSK_BINARY = os.path.join(EXTERNAL_SOFTWARE_ROOTDIR, "Ratatosk", "build", "src", "Ratatosk")
CONTIG_VALIDATOR_DIR = os.path.join(EXTERNAL_SOFTWARE_ROOTDIR, "ContigValidator")
CONVERT_TO_GFA_BINARY = os.path.join(EXTERNAL_SOFTWARE_SCRIPTS_DIR, "convertToGFA.py")
SDSL_DIR = os.path.join(EXTERNAL_SOFTWARE_ROOTDIR, "sdsl-lite")
MDBG_DIR = os.path.join(EXTERNAL_SOFTWARE_ROOTDIR, "rust-mdbg")
MDBG_CARGO_TOML = os.path.join(MDBG_DIR, "Cargo.toml")
MDBG_BINARY = os.path.join(MDBG_DIR, "target", "release", "rust-mdbg")
MDBG_SIMPLIFY = os.path.join(MDBG_DIR, "utils", "magic_simplify")
MDBG_MULTI_K = os.path.join(MDBG_DIR, "utils", "multik")
LJA_DIR = os.path.join(EXTERNAL_SOFTWARE_ROOTDIR, "LJA")
LJA_BINARY = os.path.join(LJA_DIR, "bin", "lja")
HIFIASM_DIR = os.path.join(EXTERNAL_SOFTWARE_ROOTDIR, "hifiasm")
HIFIASM_BINARY = os.path.join(HIFIASM_DIR, "hifiasm")
HOMOPOLYMER_COMPRESS_RS_DIR = os.path.join(EXTERNAL_SOFTWARE_ROOTDIR, "homopolymer-compress-rs")
HOMOPOLYMER_COMPRESS_RS_BINARY = os.path.join(HOMOPOLYMER_COMPRESS_RS_DIR, "target", "release", "homopolymer-compress")
WTDBG2_HOMOPOLYMER_DECOMPRESSION_DIR = os.path.join(EXTERNAL_SOFTWARE_ROOTDIR, "wtdbg2-homopolymer-decompression")
WTDBG2_HOMOPOLYMER_DECOMPRESSION_BINARY = os.path.join(WTDBG2_HOMOPOLYMER_DECOMPRESSION_DIR, "target", "release", "wtdbg2-homopolymer-decompression")
HISIM_DIR = os.path.join(EXTERNAL_SOFTWARE_ROOTDIR, "HI.SIM")
HISIM_MODEL_BINARY = os.path.join(HISIM_DIR, "HImodel")
HISIM_SIM_BINARY = os.path.join(HISIM_DIR, "HIsim")
HISIM_FASTA_BINARY = os.path.join(HISIM_DIR, "HIfasta")
FASTK_DIR = os.path.join(EXTERNAL_SOFTWARE_ROOTDIR, "FASTK")
FASTK_BINARY = os.path.join(FASTK_DIR, "FastK")
FASTK_SYMMEX_BINARY = os.path.join(FASTK_DIR, "Symmex")
FASTK_HISTEX_BINARY = os.path.join(FASTK_DIR, "Histex")
# TODO remove
ALGORITHM_PREFIX_FORMAT = os.path.join(DATADIR, "algorithms", "{arguments}")
#################################
###### Global report rules ######
#################################
localrules: do_nothing
rule do_nothing:
shell: "echo 'No target specified'"
def get_all_report_files():
try:
result = []
for report_name, report_definition in reports.items():
for report_file_name, report_file_definition in report_definition["report_files"].items():
report_file_arguments = report_file_definition.arguments
#print(f"report_name: {report_name}")
#print(f"report_file_arguments: {report_file_arguments}", flush = True)
result.append(REPORT_PDF.format(report_name = report_name, report_file_name = str(report_file_arguments)))
for aggregated_report_name in aggregated_reports.keys():
result.append(AGGREGATED_REPORT_PDF.format(aggregated_report_name = aggregated_report_name))
return result
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
localrules: report_all
rule report_all:
input: get_all_report_files(),
threads: 1
resources: mail_type = "END,FAIL,INVALID_DEPEND,REQUEUE"
def get_test_report_files():
try:
result = []
for report_name, report_definition in reports.items():
if not report_name.startswith("E.coli_HiFi"):
continue
for report_file_name, report_file_definition in report_definition["report_files"].items():
report_file_arguments = report_file_definition.arguments
#print(f"report_file_arguments: {report_file_arguments}", flush = True)
result.append(REPORT_PDF.format(report_name = report_name, report_file_name = str(report_file_arguments)))
for aggregated_report_name in aggregated_reports.keys():
result.append(AGGREGATED_REPORT_PDF.format(aggregated_report_name = aggregated_report_name))
return result
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
localrules: report_test
rule report_test:
input: get_test_report_files(),
threads: 1
resources: mail_type = "END,FAIL,INVALID_DEPEND,REQUEUE"
###############################
###### Report Generation ######
###############################
### Create single report ###
def get_report_file(report_name, report_file_name):
try:
if report_name not in reports:
raise Exception("report_name not in reports: {}".format(report_name))
report_files = reports[report_name]["report_files"]
if report_file_name not in report_files:
raise Exception("report_file_name not in report_files: {}".format(report_file_name))
return report_files[report_file_name]
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
def get_report_file_quasts(report_name, report_file_name):
try:
report_file = get_report_file(report_name, report_file_name)
quasts = []
for column in report_file.columns:
#print(f"QUAST_OUTPUT_DIR: {QUAST_OUTPUT_DIR}")
#print(f"column.arguments: {column.arguments}", flush = True)
assembler = column.arguments.assembler_name()
assembler_argument_string = ASSEMBLER_ARGUMENT_STRINGS[assembler]
#print(assembler_argument_string, flush = True)
assembler_arguments = column.arguments.assembler_arguments()
#print(f"raw assembler_arguments: {assembler_arguments}", flush = True)
assembler_arguments.setdefault("retain_cm", column.arguments["retain_cm"])
#print(f"completed assembler_arguments: {assembler_arguments}", flush = True)
assembler_arguments = assembler_argument_string.format(**assembler_arguments)
#print(f"serialised assembler_arguments: {assembler_arguments}", flush = True)
quasts.append(safe_format(QUAST_OUTPUT_DIR, assembler = assembler, assembler_arguments = assembler_arguments).format(**column.arguments))
return quasts
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
def get_report_file_quasts_from_wildcards(wildcards):
try:
return get_report_file_quasts(wildcards.report_name, wildcards.report_file_name)
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
def get_report_file_resources_evaluations_from_wildcards(wildcards):
try:
report_name = wildcards.report_name
report_file_name = wildcards.report_file_name
report_file = get_report_file(report_name, report_file_name)
result = []
for column in report_file.columns:
#print(RESOURCES_EVALUATION)
#print(column.arguments, flush = True)
assembler = column.arguments.assembler_name()
assembler_argument_string = ASSEMBLER_ARGUMENT_STRINGS[assembler]
#print(assembler_argument_string, flush = True)
#print(column.arguments.assembler_arguments(), flush = True)
assembler_arguments = assembler_argument_string.format(**column.arguments.assembler_arguments())
#print(assembler_arguments, flush = True)
result.append(safe_format(RESOURCES_EVALUATION, assembler = assembler, assembler_arguments = assembler_arguments).format(**column.arguments))
return result
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
def get_report_file_column_shortnames(report_name, report_file_name):
try:
report_file = get_report_file(report_name, report_file_name)
shortnames = []
for column in report_file.columns:
shortnames.append(column.shortname)
return shortnames
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
def get_report_file_column_shortnames_from_wildcards(wildcards):
try:
return get_report_file_column_shortnames(wildcards.report_name, wildcards.report_file_name)
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
def get_report_genome_names(report_name, report_file_name):
try:
report_file = get_report_file(report_name, report_file_name)
genome_names = set()
for column in report_file.columns:
genome = column.genome
genome_names.add(genome)
return genome_names
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
def get_report_genome_names_from_wildcards(wildcards):
try:
return get_report_genome_names(wildcards.report_name, wildcards.report_file_name)
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
def get_single_report_script_column_arguments(report_name, report_file_name):
try:
report_file = get_report_file(report_name, report_file_name)
result = ""
once = True
for column in report_file.columns:
if once:
once = False
else:
result += " "
assembler = column.arguments.assembler_name()
assembler_argument_string = ASSEMBLER_ARGUMENT_STRINGS[assembler]
assembler_arguments = assembler_argument_string.format(**column.arguments.assembler_arguments())
quast_output_dir = safe_format(QUAST_OUTPUT_DIR, assembler = assembler, assembler_arguments = assembler_arguments).format(**column.arguments)
resources_evaluation_file = safe_format(RESOURCES_EVALUATION, assembler = assembler, assembler_arguments = assembler_arguments).format(**column.arguments)
result += f"'{column.shortname}' '' '{quast_output_dir}' '' '{resources_evaluation_file}'"
return result
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
def get_single_report_script_column_arguments_from_wildcards(wildcards):
try:
return get_single_report_script_column_arguments(wildcards.report_name, wildcards.report_file_name)
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
rule create_single_report_tex:
input: quasts = get_report_file_quasts_from_wildcards,
combined_eaxmax_plot = REPORT_COMBINED_EAXMAX_PLOT,
resources_evaluations = get_report_file_resources_evaluations_from_wildcards,
script = CONVERT_VALIDATION_OUTPUTS_TO_LATEX_SCRIPT,
output: report = REPORT_TEX,
params: genome_name = lambda wildcards: ", ".join(get_report_genome_names_from_wildcards(wildcards)),
script_column_arguments = get_single_report_script_column_arguments_from_wildcards,
name_file = REPORT_NAME_FILE,
hashdir = REPORT_HASHDIR,
wildcard_constraints:
report_name = "[^/]+",
conda: "config/conda-latex-gen-env.yml"
threads: 1
shell: """
mkdir -p '{params.hashdir}'
echo '{wildcards.report_name} {params.genome_name} {wildcards.report_file_name}' > '{params.name_file}'
python3 '{input.script}' '{params.hashdir}' '{params.name_file}' 'none' 'none' '{input.combined_eaxmax_plot}' '{output}' {params.script_column_arguments}
"""
### Create aggregated report ###
def get_aggregated_report_file_maps(aggregated_report_name):
try:
result = {}
for report_name in aggregated_reports[aggregated_report_name]["reports"]:
result.setdefault(report_name, {}).update(reports[report_name]["report_files"])
return result
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
def iterate_aggregated_report_file_source_reports(aggregated_report_name):
try:
aggregated_report_files = get_aggregated_report_file_maps(aggregated_report_name)
for report_name, report_file_map in aggregated_report_files.items():
for report_file_name, report_file_definition in report_file_map.items():
yield (report_name, report_file_name)
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
def iterate_aggregated_report_file_source_reports_short_names(aggregated_report_name):
try:
aggregated_report_files = get_aggregated_report_file_maps(aggregated_report_name)
for report_name, report_file_map in aggregated_report_files.items():
for report_file_name, report_file_definition in report_file_map.items():
yield (report_name, report_file_definition.shortname)
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
def get_aggregated_report_file_source_report_paths(aggregated_report_name):
try:
result = []
for report_name, report_file_name in iterate_aggregated_report_file_source_reports(aggregated_report_name):
result.append(REPORT_PREFIX_FORMAT.format(report_name = report_name, report_file_name = report_file_name) + "report.tex")
return result
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
def get_aggregated_report_file_source_report_paths_from_wildcards(wildcards):
try:
return get_aggregated_report_file_source_report_paths(wildcards.aggregated_report_name)
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
rule create_aggregated_report_tex:
input: source_reports = get_aggregated_report_file_source_report_paths_from_wildcards,
script = "scripts/create_aggregated_wtdbg2_report.py",
output: file = AGGREGATED_REPORT_PDF,
params: source_reports_arg = lambda wildcards: "' '".join(get_aggregated_report_file_source_report_paths_from_wildcards(wildcards)),
source_report_names_arg = lambda wildcards: "' '".join([report_name + "/" + report_file_name for report_name, report_file_name in iterate_aggregated_report_file_source_reports_short_names(wildcards.aggregated_report_name)]),
wildcard_constraints:
report_name = "[^/]+",
conda: "config/conda-latex-gen-env.yml"
threads: 1
shell: """
python3 '{input.script}' --source-reports '{params.source_reports_arg}' --source-report-names '{params.source_report_names_arg}' --output '{output.file}'
"""
rule create_combined_eaxmax_graph:
input: quast_csvs = lambda wildcards: [os.path.join(q, "aligned_stats", "EAxmax_plot.csv") for q in get_report_file_quasts_from_wildcards(wildcards)],
script = CREATE_COMBINED_EAXMAX_PLOT_SCRIPT,
output: REPORT_COMBINED_EAXMAX_PLOT,
params: input_quast_csvs = lambda wildcards, input: "' '".join([shortname + "' '" + quast for shortname, quast in zip(get_report_file_column_shortnames_from_wildcards(wildcards), input.quast_csvs)])
wildcard_constraints:
report_name = "[^/]+",
conda: "config/conda-seaborn-env.yml"
threads: 1
shell: """
mkdir -p "$(dirname '{output}')"
python3 '{input.script}' '{params.input_quast_csvs}' '{output}'
"""
rule png_to_pdf:
input: "{file}.png"
output: "{file}.image.pdf"
conda: "config/conda-imagemagick-env.yml"
threads: 1
shell: "convert {input} {output}"
rule latex:
input: "{subpath}report.tex"
output: "{subpath}report.pdf"
conda: "config/conda-latex-env.yml"
threads: 1
shell: """
tectonic '{input}'
"""
# def get_genome_reads_from_wildcards(wildcards):
# try:
# arguments = Arguments.from_str(wildcards.arguments)
# if arguments.read_simulator_name() is None or arguments.read_simulator_name() == "none":
# return GENOME_READS_FORMAT.format(genome = arguments["genome"])
# else:
# return GENOME_SIMULATED_READS_FASTA_FORMAT.format(genome = arguments["genome"], read_simulator_name = arguments.read_simulator_name(), read_simulator_arguments = arguments.read_simulator_arguments())
# except Exception:
# traceback.print_exc()
# sys.exit("Catched exception")
# def get_genome_reference_from_wildcards(wildcards):
# try:
# arguments = Arguments.from_str(wildcards.arguments)
# return GENOME_REFERENCE_FORMAT.format(genome = arguments["genome"])
# except Exception:
# traceback.print_exc()
# sys.exit("Catched exception")
# rule find_wtdbg2_node_errors:
# input: nodes = os.path.join(WTDBG2_OUTPUT_DIR_PACKED, "wtdbg2.1.nodes"),
# reference = GENOME_REFERENCE,
# script = "scripts/find_wtdbg2_node_errors.py",
# output: deviation_histogram = os.path.join(ASSEMBLY_OUTPUT_DIR, "wtdbg2_node_errors", "deviation_histogram.pdf"),
# log: log = os.path.join(ALGORITHM_PREFIX_FORMAT, "wtdbg2_node_errors", "wtdbg2_node_errors.log"),
# params: output_prefix = os.path.join(ALGORITHM_PREFIX_FORMAT, "wtdbg2_node_errors") + "/",
# conda: "config/conda-wtdbg2-node-errors-env.yml"
# threads: 1
# shell: "PYTHONUNBUFFERED=1 '{input.script}' '{input.nodes}' '{input.reference}' '{params.output_prefix}' 2>&1 | tee '{log.log}'"
########################
###### Injections ######
########################
def get_injectable_contigs_rust_cli_command_from_wildcards(wildcards):
try:
injection = wildcards.tig_injection
if "unitigs" == injection:
return "compute-unitigs"
elif "trivial_omnitigs" == injection:
return "compute-trivial-omnitigs --non-scc"
elif "omnitigs" == injection:
return "compute-omnitigs --linear-reduction"
else:
raise Exception(f"Wrong injection command in assembler arguments: {wildcards}")
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
rule compute_injectable_contigs_wtdbg2:
input: nodes = safe_format(os.path.join(WTDBG2_OUTPUT_DIR, "wtdbg2.3.nodes"), tig_injection = "none"),
reads = safe_format(os.path.join(WTDBG2_OUTPUT_DIR, "wtdbg2.3.reads"), tig_injection = "none"),
dot = safe_format(os.path.join(WTDBG2_OUTPUT_DIR, "wtdbg2.3.dot"), tig_injection = "none"),
raw_reads = GENOME_READS,
binary = RUST_BINARY,
output: file = os.path.join(WTDBG2_INJECTABLE_CONTIG_DIR, "contigwalks.ssv"),
latex = os.path.join(WTDBG2_INJECTABLE_CONTIG_DIR, "compute_injectable_contigs.tex"),
log: log = os.path.join(WTDBG2_INJECTABLE_CONTIG_DIR, "compute_injectable_contigs.log"),
params: command = get_injectable_contigs_rust_cli_command_from_wildcards,
threads: 1
resources: mem_mb = 48000
shell: "${{CONDA_PREFIX}}/bin/time -v '{input.binary}' {params.command} --output-as-wtdbg2-node-ids --file-format wtdbg2 --input '{input.nodes}' --input '{input.reads}' --input '{input.raw_reads}' --input '{input.dot}' --output '{output.file}' --latex '{output.latex}' 2>&1 | tee '{log.log}'"
def get_injectable_fragment_contigs_rust_cli_command_from_wildcards(wildcards):
try:
injection = wildcards.frg_injection
if "unitigs" == injection:
return "compute-unitigs"
elif "trivial_omnitigs" == injection:
return "compute-trivial-omnitigs --non-scc"
elif "omnitigs" == injection:
return "compute-omnitigs --linear-reduction"
else:
raise Exception("Wrong injection command in assembler arguments: {wildcards}")
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
rule compute_injectable_fragment_contigs_wtdbg2:
input: dot = lambda wildcards: safe_format(os.path.join(WTDBG2_OUTPUT_DIR, f"wtdbg2.{wildcards.frg_injection_stage}.dot"), frg_injection = "none", frg_injection_stage = "none"),
binary = RUST_BINARY,
output: file = os.path.join(WTDBG2_INJECTABLE_FRAGMENT_CONTIG_DIR, "contigwalks.ssv"),
latex = os.path.join(WTDBG2_INJECTABLE_FRAGMENT_CONTIG_DIR, "compute_injectable_contigs.tex"),
log: log = os.path.join(WTDBG2_INJECTABLE_FRAGMENT_CONTIG_DIR, "compute_injectable_contigs.log"),
params: command = get_injectable_fragment_contigs_rust_cli_command_from_wildcards,
threads: 1
resources: mem_mb = 48000
shell: "${{CONDA_PREFIX}}/bin/time -v '{input.binary}' {params.command} --file-format dot --input '{input.dot}' --output '{output.file}' --latex '{output.latex}' 2>&1 | tee '{log.log}'"
#################################
###### Postprocess Contigs ######
#################################
def get_raw_assembly_file_from_wildcards(wildcards):
try:
arguments = Arguments.from_str(wildcards.arguments)
assembler_name = arguments.assembler_name()
if assembler_name == "flye":
result = ALGORITHM_PREFIX_FORMAT + "flye/assembly.fasta"
elif assembler_name == "wtdbg2":
result = WTDBG2_PREFIX_FORMAT + "wtdbg2.raw.fa"
elif assembler_name == "hifiasm":
result = os.path.join(HIFIASM_PREFIX_FORMAT, "assembly.p_ctg.fa")
elif assembler_name == "reference":
result = GENOME_REFERENCE_FORMAT
else:
raise Exception("Unknown assembler {} in arguments: {}".format(assembler_name, arguments))
arguments.retain_raw_assembly_arguments()
return result.format(genome = arguments.genome(), arguments = str(arguments))
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
localrules: select_assembler
rule select_assembler:
input: raw_assembly_from_assembler = get_raw_assembly_file_from_wildcards,
output: raw_assembly = ALGORITHM_PREFIX_FORMAT + "raw_assembly.fa",
threads: 1
shell: "ln -sr '{input.raw_assembly_from_assembler}' '{output.raw_assembly}'"
def get_raw_gfa_assembly_file_from_wildcards(wildcards):
try:
arguments = Arguments.from_str(wildcards.arguments)
assembler_name = arguments.assembler_name()
if assembler_name == "hifiasm":
result = os.path.join(HIFIASM_PREFIX_FORMAT, "hifiasm", "assembly.r_utg.gfa")
else:
raise Exception("Assembler {} does not support gfa (in arguments: {})".format(assembler_name, arguments))
arguments.retain_raw_assembly_arguments()
return result.format(genome = arguments.genome(), arguments = str(arguments))
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
localrules: select_gfa_assembler
rule select_gfa_assembler:
input: raw_assembly_from_assembler = get_raw_gfa_assembly_file_from_wildcards,
output: raw_assembly = ALGORITHM_PREFIX_FORMAT + "raw_assembly.gfa",
threads: 1
shell: "ln -sr '{input.raw_assembly_from_assembler}' '{output.raw_assembly}'"
def get_assembly_postprocessing_target_file_from_wildcards(wildcards):
try:
try:
arguments = Arguments.from_str(wildcards.arguments)
except json.decoder.JSONDecodeError:
traceback.print_exc()
raise Exception("JSONDecodeError: {}".format(wildcards.arguments))
postprocessor_name = arguments.postprocessor_name()
if postprocessor_name == "contigbreaker":
return ALGORITHM_PREFIX_FORMAT + "contigbreaker/broken_contigs.fa"
elif postprocessor_name == "gfa_trivial_omnitigs":
return os.path.join(ALGORITHM_PREFIX_FORMAT, "gfa_trivial_omnitigs/trivial_omnitigs.fa")
else:
return ALGORITHM_PREFIX_FORMAT + "raw_assembly.fa"
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
localrules: request_assembly_postprocessing
rule request_assembly_postprocessing:
input: get_assembly_postprocessing_target_file_from_wildcards
output: assembly = ALGORITHM_PREFIX_FORMAT + "assembly.fa"
threads: 1
shell: "ln -sr '{input}' '{output}'"
def get_source_genome_properties_from_wildcards(wildcards):
try:
if hasattr(wildcards, "genome"):
genome_name = wildcards.genome
elif hasattr(wildcards, "corrected_genome"):
genome_name = wildcards.corrected_genome
elif hasattr(wildcards, "arguments"):
arguments = Arguments.from_str(wildcards.arguments)
genome_name = arguments.genome()
if genome_name is None:
raise Exception("Arguments has no 'genome' attribute: {}".format(arguments))
else:
raise Exception("Wildcards has no 'genome', 'corrected_genome' or 'arguments' attribute")
if genome_name in genomes:
pass
elif corrected_genomes is not None and genome_name in corrected_genomes:
genome_name = corrected_genomes[genome_name]["source_genome"]
else:
raise Exception("Genome name not found: " + str(genome_name))
return genomes[genome_name]
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
def compute_genome_mem_mb_from_wildcards(wildcards, base_mem_mb):
try:
genome_properties = get_source_genome_properties_from_wildcards(wildcards)
if "assembly_mem_factor" in genome_properties:
return int(float(genome_properties["assembly_mem_factor"]) * float(base_mem_mb))
else:
return base_mem_mb
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
def compute_genome_time_min_from_wildcards(wildcards, base_time_min):
try:
genome_properties = get_source_genome_properties_from_wildcards(wildcards)
if "assembly_time_factor" in genome_properties:
if hasattr(wildcards, "read_source") and wildcards.read_source.startswith("hisim_"):
return int(float(genome_properties["assembly_time_factor"]) * float(base_time_min)) * 2
else:
return int(float(genome_properties["assembly_time_factor"]) * float(base_time_min))
else:
return base_time_min
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
def compute_genome_queue_from_wildcards(wildcards, base_time_min, base_mem_mb = 0):
try:
time = compute_genome_time_min_from_wildcards(wildcards, base_time_min)
mem = compute_genome_mem_mb_from_wildcards(wildcards, base_mem_mb)
cluster = compute_genome_cluster_from_wildcards(wildcards, base_time_min, base_mem_mb)
if cluster == "ukko":
if mem >= 250_000:
if time <= 1440 * 3:
return "bigmem,aurinko"
else:
return "aurinko"
elif time <= 60 * 8:
return "short,medium,bigmem,aurinko"
elif time <= 1440 * 2:
return "medium,bigmem,aurinko"
elif time <= 1440 * 3:
return "bigmem,aurinko"
else:
return "aurinko" # aurinko can handle anything
#else:
# sys.exit("No applicable queue for runtime " + str(time) + " (wildcards: " + str(wildcards) + ")")
elif cluster == "kale":
raise Exception("kale disabled")
if mem >= 380_000:
return "bigmem"
elif time <= 1440:
return "short,medium,long,bigmem"
elif time <= 1440 * 7:
return "medium,long,bigmem"
elif time <= 1440 * 14:
return "long,bigmem"
else:
sys.exit("No applicable queue for runtime " + str(time) + " (wildcards: " + str(wildcards) + ")")
else:
sys.exit("No applicable cluster for runtime " + str(time) + " (wildcards: " + str(wildcards) + ")")
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
def compute_genome_cluster_from_wildcards(wildcards, base_time_min, base_mem_mb = 0):
try:
time = compute_genome_time_min_from_wildcards(wildcards, base_time_min)
mem = compute_genome_mem_mb_from_wildcards(wildcards, base_mem_mb)
#if time <= 1440 * 2:
# return "ukko"
#elif time <= 1440 * 14:
# return "kale"
#else:
# sys.exit("No applicable cluster for runtime " + str(time) + " (wildcards: " + str(wildcards) + ")")
return "ukko" # run everything on ukko for now, using aurinko for long jobs
except Exception:
traceback.print_exc()
sys.exit("Catched exception")
rule run_contigbreaker:
input: contigs = ALGORITHM_PREFIX_FORMAT + "raw_assembly.fa",
reads = GENOME_READS,
script = "tools/contigbreaker/contigbreaker.py"
output: broken_contigs = ALGORITHM_PREFIX_FORMAT + "contigbreaker/broken_contigs.fa",
completed = touch(ALGORITHM_PREFIX_FORMAT + "contigbreaker/broken_contigs.fa.completed"),
threads: MAX_THREADS
resources: mem_mb = lambda wildcards: compute_genome_mem_mb_from_wildcards(wildcards, 60_000),
time_min = lambda wildcards: compute_genome_time_min_from_wildcards(wildcards, 720),
cpus = MAX_THREADS,
queue = lambda wildcards: compute_genome_queue_from_wildcards(wildcards, 720, 60_000),
cluster = lambda wildcards: compute_genome_cluster_from_wildcards(wildcards, 720, 60_000),
conda: "tools/contigbreaker/environment.yml"
shell: "'{input.script}' --threads {threads} --input-contigs '{input.contigs}' --input-reads '{input.reads}' --output-contigs '{output.broken_contigs}'"
rule run_gfa_trivial_omnitigs:
input: contigs = os.path.join(ALGORITHM_PREFIX_FORMAT, "raw_assembly.gfa"),
binary = RUST_BINARY,
output: trivial_omnitigs = os.path.join(ALGORITHM_PREFIX_FORMAT, "gfa_trivial_omnitigs", "trivial_omnitigs.fa"),
log: log = os.path.join(ALGORITHM_PREFIX_FORMAT, "gfa_trivial_omnitigs", "trivial_omnitigs.log"),
threads: 1
resources:
mem_mb = lambda wildcards: compute_genome_mem_mb_from_wildcards(wildcards, 10_000),
time_min = lambda wildcards: compute_genome_time_min_from_wildcards(wildcards, 60),
cpus = 1,
queue = lambda wildcards: compute_genome_queue_from_wildcards(wildcards, 60, 10_000),
cluster = lambda wildcards: compute_genome_cluster_from_wildcards(wildcards, 60, 10_000),
shell: "'{input.binary}' compute-trivial-omnitigs --non-scc --file-format hifiasm --input '{input.contigs}' --output '{output.trivial_omnitigs}' 2>&1 | tee '{log.log}'"
####################
###### wtdbg2 ######
####################
rule wtdbg2:
input: reads = GENOME_READS,
reference_length = safe_format(GENOME_REFERENCE_LENGTH, filter_nw = "no", retain_cm = "no", filter_plasmids = "no"),
binary = WTDBG2_BINARY,
output: original_nodes = os.path.join(WTDBG2_OUTPUT_DIR, "wtdbg2.1.nodes"),
nodes = os.path.join(WTDBG2_OUTPUT_DIR, "wtdbg2.3.nodes"),
reads = os.path.join(WTDBG2_OUTPUT_DIR, "wtdbg2.3.reads"),
dot = os.path.join(WTDBG2_OUTPUT_DIR, "wtdbg2.3.dot.gz"),
ctg_dot = os.path.join(WTDBG2_OUTPUT_DIR, "wtdbg2.ctg.dot.gz"),
clips = os.path.join(WTDBG2_OUTPUT_DIR, "wtdbg2.clps"),
kbm = os.path.join(WTDBG2_OUTPUT_DIR, "wtdbg2.kbm"),
ctg_lay = os.path.join(WTDBG2_OUTPUT_DIR, "wtdbg2.ctg.lay.gz"),
frg_dot = [os.path.join(WTDBG2_OUTPUT_DIR, "wtdbg2.{}.frg.dot.gz".format(i)) for i in range(1, 11)],
log: log = WTDBG2_LOG,
params: output_prefix = os.path.join(WTDBG2_OUTPUT_DIR, "wtdbg2"),
fragment_correction_steps = lambda wildcards: f"--fragment-correction-steps {wildcards.fragment_correction_steps}" if wildcards.fragment_correction_steps != "all" else "",
wildcard_constraints:
tig_injection = "none",
frg_injection = "none",
frg_injection_stage = "none",
skip_fragment_assembly = "no",
threads: MAX_THREADS
resources: mem_mb = lambda wildcards: compute_genome_mem_mb_from_wildcards(wildcards, 100_000),
cpus = MAX_THREADS,
time_min = lambda wildcards: compute_genome_time_min_from_wildcards(wildcards, 720),
queue = lambda wildcards: compute_genome_queue_from_wildcards(wildcards, 720, 100_000),
cluster = lambda wildcards: compute_genome_cluster_from_wildcards(wildcards, 720, 100_000),
shell: """
read -r REFERENCE_LENGTH < '{input.reference_length}'
${{CONDA_PREFIX}}/bin/time -v '{input.binary}' -x {wildcards.wtdbg2_mode} -g $REFERENCE_LENGTH -i '{input.reads}' -t {threads} -fo '{params.output_prefix}' --dump-kbm '{output.kbm}' {params.fragment_correction_steps} 2>&1 | tee '{log.log}'
"""
rule wtdbg2_skip_fragment_assembly:
input: reads = GENOME_READS,
reference_length = safe_format(GENOME_REFERENCE_LENGTH, filter_nw = "no", retain_cm = "no", filter_plasmids = "no"),
binary = WTDBG2_BINARY,
output: original_nodes = os.path.join(WTDBG2_OUTPUT_DIR, "wtdbg2.1.nodes"),
nodes = os.path.join(WTDBG2_OUTPUT_DIR, "wtdbg2.3.nodes"),
reads = os.path.join(WTDBG2_OUTPUT_DIR, "wtdbg2.3.reads"),
dot = os.path.join(WTDBG2_OUTPUT_DIR, "wtdbg2.3.dot.gz"),
ctg_dot = os.path.join(WTDBG2_OUTPUT_DIR, "wtdbg2.ctg.dot.gz"),
clips = os.path.join(WTDBG2_OUTPUT_DIR, "wtdbg2.clps"),
kbm = os.path.join(WTDBG2_OUTPUT_DIR, "wtdbg2.kbm"),
ctg_lay = os.path.join(WTDBG2_OUTPUT_DIR, "wtdbg2.ctg.lay.gz"),
log: log = WTDBG2_LOG,
params: output_prefix = os.path.join(WTDBG2_OUTPUT_DIR, "wtdbg2"),
fragment_correction_steps = lambda wildcards: f"--fragment-correction-steps {wildcards.fragment_correction_steps}" if wildcards.fragment_correction_steps != "all" else "",
wildcard_constraints:
tig_injection = "none",
frg_injection = "none",
frg_injection_stage = "none",
skip_fragment_assembly = "yes",
threads: MAX_THREADS
resources: mem_mb = lambda wildcards: compute_genome_mem_mb_from_wildcards(wildcards, 100_000),
cpus = MAX_THREADS,
time_min = lambda wildcards: compute_genome_time_min_from_wildcards(wildcards, 720),
queue = lambda wildcards: compute_genome_queue_from_wildcards(wildcards, 720, 100_000),
cluster = lambda wildcards: compute_genome_cluster_from_wildcards(wildcards, 720, 100_000),
shell: """
read -r REFERENCE_LENGTH < '{input.reference_length}'