def _variant_checkpoints(samples): """Check sample configuration to identify required steps in analysis. """ checkpoints = {} checkpoints["vc"] = any([dd.get_variantcaller(d) for d in samples]) checkpoints["sv"] = any([dd.get_svcaller(d) for d in samples]) checkpoints["jointvc"] = any([(dd.get_jointcaller(d) or ("gvcf" in dd.get_tools_on(d))) and dd.get_batch(d) for d in samples]) checkpoints["hla"] = any([dd.get_hlacaller(d) for d in samples]) checkpoints["align"] = any([(dd.get_aligner(d) or dd.get_bam_clean(d)) for d in samples]) checkpoints["align_split"] = not all([(dd.get_align_split_size(d) is False or not dd.get_aligner(d)) for d in samples]) return checkpoints
def _variant_checkpoints(samples): """Check sample configuration to identify required steps in analysis. """ checkpoints = {} checkpoints["vc"] = any([dd.get_variantcaller(d) or d.get("vrn_file") for d in samples]) checkpoints["sv"] = any([dd.get_svcaller(d) for d in samples]) checkpoints["jointvc"] = any([(dd.get_jointcaller(d) or "gvcf" in dd.get_tools_on(d)) for d in samples]) checkpoints["hla"] = any([dd.get_hlacaller(d) for d in samples]) checkpoints["align"] = any([(dd.get_aligner(d) or dd.get_bam_clean(d)) for d in samples]) checkpoints["align_split"] = not all([(dd.get_align_split_size(d) is False or not dd.get_aligner(d)) for d in samples]) checkpoints["umi"] = any([dd.get_umi_consensus(d) for d in samples]) checkpoints["ensemble"] = any([dd.get_ensemble(d) for d in samples]) checkpoints["cancer"] = any(dd.get_phenotype(d) in ["tumor"] for d in samples) return checkpoints
def _variant_checkpoints(samples): """Check sample configuration to identify required steps in analysis. """ checkpoints = {} checkpoints["vc"] = any([dd.get_variantcaller(d) or d.get("vrn_file") for d in samples]) checkpoints["sv"] = any([dd.get_svcaller(d) for d in samples]) checkpoints["jointvc"] = any([(dd.get_jointcaller(d) or "gvcf" in dd.get_tools_on(d)) for d in samples]) checkpoints["hla"] = any([dd.get_hlacaller(d) for d in samples]) checkpoints["align"] = any([(dd.get_aligner(d) or dd.get_bam_clean(d)) for d in samples]) checkpoints["align_split"] = not all([(dd.get_align_split_size(d) is False or not dd.get_aligner(d)) for d in samples]) checkpoints["archive"] = any([dd.get_archive(d) for d in samples]) checkpoints["umi"] = any([dd.get_umi_consensus(d) for d in samples]) checkpoints["ensemble"] = any([dd.get_ensemble(d) for d in samples]) checkpoints["cancer"] = any(dd.get_phenotype(d) in ["tumor"] for d in samples) return checkpoints