def add_reference_resources(data, remote_retriever=None): """Add genome reference information to the item to process. """ aligner = data["config"]["algorithm"].get("aligner", None) if remote_retriever: data["reference"] = remote_retriever.get_refs(data["genome_build"], aligner, data["config"]) else: data["reference"] = genome.get_refs(data["genome_build"], aligner, data["dirs"]["galaxy"], data) _check_ref_files(data["reference"], data) # back compatible `sam_ref` target data["sam_ref"] = utils.get_in(data, ("reference", "fasta", "base")) ref_loc = utils.get_in(data, ("config", "resources", "species", "dir"), utils.get_in(data, ("reference", "fasta", "base"))) if remote_retriever: data = remote_retriever.get_resources(data["genome_build"], ref_loc, data) else: data["genome_resources"] = genome.get_resources(data["genome_build"], ref_loc, data) data["genome_resources"] = genome.add_required_resources(data["genome_resources"]) if effects.get_type(data) == "snpeff" and "snpeff" not in data["reference"]: data["reference"]["snpeff"] = effects.get_snpeff_files(data) if "genome_context" not in data["reference"]: data["reference"]["genome_context"] = annotation.get_context_files(data) if "viral" not in data["reference"]: data["reference"]["viral"] = viral.get_files(data) data = _fill_validation_targets(data) data = _fill_prioritization_targets(data) data = _fill_capture_regions(data) # Re-enable when we have ability to re-define gemini configuration directory if False: if population.do_db_build([data], need_bam=False): data["reference"]["gemini"] = population.get_gemini_files(data) return data
def add_reference_resources(data, remote_retriever=None): """Add genome reference information to the item to process. """ aligner = data["config"]["algorithm"].get("aligner", None) if remote_retriever: data["reference"] = remote_retriever.get_refs(data["genome_build"], aligner, data["config"]) else: data["reference"] = genome.get_refs(data["genome_build"], aligner, data["dirs"]["galaxy"], data) _check_ref_files(data["reference"], data) # back compatible `sam_ref` target data["sam_ref"] = utils.get_in(data, ("reference", "fasta", "base")) ref_loc = utils.get_in(data, ("config", "resources", "species", "dir"), utils.get_in(data, ("reference", "fasta", "base"))) if remote_retriever: data = remote_retriever.get_resources(data["genome_build"], ref_loc, data) else: data["genome_resources"] = genome.get_resources(data["genome_build"], ref_loc, data) data["genome_resources"] = genome.add_required_resources(data["genome_resources"]) if effects.get_type(data) == "snpeff" and "snpeff" not in data["reference"]: data["reference"]["snpeff"] = effects.get_snpeff_files(data) if "genome_context" not in data["reference"]: data["reference"]["genome_context"] = annotation.get_context_files(data) if "viral" not in data["reference"]: data["reference"]["viral"] = viral.get_files(data) if not data["reference"]["viral"]: data["reference"]["viral"] = None data = _fill_validation_targets(data) data = _fill_prioritization_targets(data) data = _fill_capture_regions(data) # Re-enable when we have ability to re-define gemini configuration directory if False: if population.do_db_build([data], need_bam=False): data["reference"]["gemini"] = population.get_gemini_files(data) return data