Add option to analyse only mitochondria #608
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fellen31
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Sep 24, 2024
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Could you update the docs as well, to add the new analysis_type? And if there are any changes to the output.
| emit: | ||
| vcf = SVDB_MERGE.out.vcf // channel: [ val(meta), path(vcf)] | ||
| tbi = TABIX_TABIX.out.tbi // channel: [ val(meta), path(tbi)] | ||
| vcf = ch_merged_svs // channel: [ val(meta), path(vcf)] |
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If only mito analysis is run, are no SV calls emitted?
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SV in mitochondria will be emitted, but not the nuclear genome if that's what you are asking? 😅
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Okay, so the mitochondria SVs are not input into SVDB_MERGE and emitted as ch_merged_svs, that is only the nuclear genome?
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Ah I see what you mean. That does include nuclear genome and mt genome, but the difference is those calls are in vcf format. mito analysis at the moment does not generate SV calls in vcf format. I can update the documentation to make this clear.
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I think that would be good, to clarify if the SV calls in VCF format contains MT calls or not, just as you have done for the SNV VCFs 😊
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So if you run with --analysis_type mito no VCFs are procured, only the output files from CALL_SV_MT? Or are any of MANTA, TIDDIT, GERMLINECNVCALLER or CNVNATOR be run at the same time as --analysis_type mito?
And if you run with wgs, both the output files from CALL_SV_MT, as well as mitochondrial variants in VCF format from the callers in CALL_STRUCTURAL_VARIANTS are output?
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Yupe. That's right!
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PR checklist
I have added a new analysis type (mito) to call and annotate only mitochondrial variants.
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile test_one_sample,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).