Add option to analyse only mitochondria #608
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
fellen31
reviewed
Sep 24, 2024
|
|
||
| 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)] |
There was a problem hiding this comment.
If only mito analysis is run, are no SV calls emitted?
There was a problem hiding this comment.
SV in mitochondria will be emitted, but not the nuclear genome if that's what you are asking? 😅
There was a problem hiding this comment.
Okay, so the mitochondria SVs are not input into SVDB_MERGE and emitted as ch_merged_svs, that is only the nuclear genome?
There was a problem hiding this comment.
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.
There was a problem hiding this comment.
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 😊
There was a problem hiding this comment.
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?
There was a problem hiding this comment.
Yupe. That's right!
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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).