feat: added support for sequenza (414-2) #436
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…/snappy-pipeline into 414-defining-tumor-purityploidy
mbenary
reviewed
Aug 30, 2023
| @@ -120,7 +121,7 @@ | |||
| # Default configuration somatic_targeted_seq_cnv_calling | |||
| step_config: | |||
| somatic_targeted_seq_cnv_calling: | |||
| tools: ['cnvkit'] # REQUIRED - available: 'cnvkit', 'copywriter', 'cnvetti_on_target' and 'cnvetti_off_target' | |||
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is copywriter removed as an option? The parameters are still around.
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I will change & keep copywriter in the list. All the code is there anyway, and might still be functional, except that CopywriteR is not in bioconductor/bioconda.
| -gc {snakemake.input.gc} --fasta {genome} \ | ||
| -n {snakemake.input.normal_bam} --tumor {snakemake.input.tumor_bam} \ | ||
| -C {contigs} {extra_arguments} \ | ||
| | sequenza-utils seqz_binning -s - \ |
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Is the "-s -" correct for the piping?
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Yes it is, -s means that a seqz file is expected, and - means /dev/stdin
mbenary
approved these changes
Aug 30, 2023
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Add
sequenzaas a copy number caller, instead of bundling within thehomologous_recombination_deficiencystep.Advantages:
scarHRDrelies on an obsolete version ofsequenzawhich returnsNAfor average coverage.scarHRDsequenzareport (potentially, as it isn't implemented yet)