feat: Added support for scarHRD #429
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mbenary
requested changes
Aug 22, 2023
| or not sample_pair.normal_sample.dna_ngs_library | ||
| ): | ||
| msg = ( | ||
| "INFO: sample pair for cancer bio sample {} has is missing primary" |
| The score is a proxy for holomogous recombination deficiencies scores produced from SNP arrays. | ||
| The software is described in `Sztupinszki et al.<https://doi.org/10.1038/s41523-018-0066-6>`, | ||
| but it is not part of CRAN, Bioconductor or bioconda (currently). | ||
| The implementation also relies on obsolete version of `sequenza<https://github.com/oicr-gsi/sequenza/tree/master>` & |
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Based on this documentation, sequenza is installed from github. The install/environment is using CRAN. Please adjust documentation or installing process.
| chr_in_name = "TRUE" if snakemake.config["step_config"][step]["scarHRD"]["chr_prefix"] else "FALSE" | ||
| prefix = "chr" if snakemake.config["step_config"][step]["scarHRD"]["chr_prefix"] else "" | ||
| if genome_name == "grch37" or genome_name == "grch38": | ||
| chromosomes = " ".join([prefix + str(x) for x in list(range(1, 25)) + ["X"]]) |
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This puzzles me ... Shouldn't it be 23? Similar for mouse.
mbenary
approved these changes
Aug 22, 2023
This was referenced Dec 9, 2024
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