def get_qc_tools(data):
"""Retrieve a list of QC tools to use based on configuration and analysis type.
Uses defaults if previously set.
"""
if dd.get_algorithm_qc(data):
return dd.get_algorithm_qc(data)
analysis = data["analysis"].lower()
to_run = []
if "fastqc" not in dd.get_tools_off(data):
to_run.append("fastqc")
if any([tool in dd.get_tools_on(data)
for tool in ["qualimap", "qualimap_full"]]):
to_run.append("qualimap")
if analysis.startswith("rna-seq"):
if gtf.is_qualimap_compatible(dd.get_gtf_file(data)):
to_run.append("qualimap_rnaseq")
else:
logger.debug("GTF not compatible with Qualimap, skipping.")
if analysis.startswith("smallrna-seq"):
to_run.append("small-rna")
if not analysis.startswith("smallrna-seq"):
to_run.append("samtools")
to_run.append("gemini")
if tz.get_in(["config", "algorithm", "kraken"], data):
to_run.append("kraken")
if analysis.startswith(("standard", "variant", "variant2")):
to_run += ["qsignature", "coverage", "variants", "picard"]
return to_run
def get_qc_tools(data):
"""Retrieve a list of QC tools to use based on configuration and analysis type.
Uses defaults if previously set.
"""
if dd.get_algorithm_qc(data):
return dd.get_algorithm_qc(data)
analysis = data["analysis"].lower()
to_run = []
if "fastqc" not in dd.get_tools_off(data):
to_run.append("fastqc")
if any([
tool in dd.get_tools_on(data)
for tool in ["qualimap", "qualimap_full"]
]):
to_run.append("qualimap")
if analysis.startswith("rna-seq"):
if gtf.is_qualimap_compatible(dd.get_gtf_file(data)):
to_run.append("qualimap_rnaseq")
else:
logger.debug("GTF not compatible with Qualimap, skipping.")
if analysis.startswith("smallrna-seq"):
to_run.append("small-rna")
if not analysis.startswith("smallrna-seq"):
to_run.append("samtools")
to_run.append("gemini")
if tz.get_in(["config", "algorithm", "kraken"], data):
to_run.append("kraken")
if analysis.startswith(("standard", "variant", "variant2")):
to_run += ["qsignature", "coverage", "variants", "picard"]
return to_run
def get_qc_tools(data):
"""Retrieve a list of QC tools to use based on configuration and analysis type.
Uses defaults if previously set.
"""
if dd.get_algorithm_qc(data):
return dd.get_algorithm_qc(data)
analysis = data["analysis"].lower()
to_run = []
if tz.get_in(["config", "algorithm", "kraken"], data):
to_run.append("kraken")
if "fastqc" not in dd.get_tools_off(data):
to_run.append("fastqc")
if any([
tool in dd.get_tools_on(data)
for tool in ["qualimap", "qualimap_full"]
]):
to_run.append("qualimap")
if analysis.startswith("rna-seq") or analysis == "smallrna-seq":
if "qualimap" not in dd.get_tools_off(data):
if gtf.is_qualimap_compatible(dd.get_gtf_file(data)):
to_run.append("qualimap_rnaseq")
else:
logger.debug("GTF not compatible with Qualimap, skipping.")
if analysis.startswith("chip-seq"):
to_run.append("chipqc")
if dd.get_chip_method(data) == "atac":
to_run.append("ataqv")
if analysis.startswith("smallrna-seq"):
to_run.append("small-rna")
to_run.append("atropos")
if "coverage_qc" not in dd.get_tools_off(data):
to_run.append("samtools")
if dd.has_variantcalls(data):
if "coverage_qc" not in dd.get_tools_off(data):
to_run += ["coverage", "picard"]
to_run += ["qsignature", "variants"]
if vcfanno.is_human(data):
to_run += ["peddy"]
if "contamination" not in dd.get_tools_off(data):
to_run += ["contamination"]
if vcfutils.get_paired_phenotype(data):
if "viral" not in dd.get_tools_off(data):
to_run += ["viral"]
if damage.should_filter([data]):
to_run += ["damage"]
if dd.get_umi_consensus(data):
to_run += ["umi"]
if tz.get_in(["config", "algorithm", "preseq"], data):
to_run.append("preseq")
to_run = [tool for tool in to_run if tool not in dd.get_tools_off(data)]
to_run.sort()
return to_run
def get_qc_tools(data):
"""Retrieve a list of QC tools to use based on configuration and analysis type.
Uses defaults if previously set.
"""
if dd.get_algorithm_qc(data):
return dd.get_algorithm_qc(data)
analysis = data["analysis"].lower()
to_run = []
if tz.get_in(["config", "algorithm", "kraken"], data):
to_run.append("kraken")
if "fastqc" not in dd.get_tools_off(data):
to_run.append("fastqc")
if any([tool in dd.get_tools_on(data)
for tool in ["qualimap", "qualimap_full"]]):
to_run.append("qualimap")
if analysis.startswith("rna-seq") or analysis == "smallrna-seq":
if "qualimap" not in dd.get_tools_off(data):
if gtf.is_qualimap_compatible(dd.get_gtf_file(data)):
to_run.append("qualimap_rnaseq")
else:
logger.debug("GTF not compatible with Qualimap, skipping.")
if analysis.startswith("chip-seq"):
to_run.append("chipqc")
if analysis.startswith("smallrna-seq"):
to_run.append("small-rna")
to_run.append("atropos")
if "coverage_qc" not in dd.get_tools_off(data):
to_run.append("samtools")
if analysis.startswith(("standard", "variant", "variant2")):
if "coverage_qc" not in dd.get_tools_off(data):
to_run += ["coverage", "picard"]
to_run += ["qsignature", "variants"]
if vcfanno.is_human(data):
to_run += ["contamination", "peddy"]
if vcfutils.get_paired_phenotype(data):
to_run += ["viral"]
if damage.should_filter([data]):
to_run += ["damage"]
if dd.get_umi_consensus(data):
to_run += ["umi"]
if tz.get_in(["config", "algorithm", "preseq"], data):
to_run.append("preseq")
to_run = [tool for tool in to_run if tool not in dd.get_tools_off(data)]
to_run.sort()
return to_run
