New module savana/to #11849
Open
manascripts wants to merge 13 commits into
Open
Conversation
SPPearce
reviewed
Jun 7, 2026
Comment on lines
+46
to
+51
| def contigs_arg = contigs ? "--contigs ${contigs}" : "" | ||
| def allele_arg = snp_vcf | ||
| ? "--snp_vcf ${snp_vcf}" | ||
| : g1000_vcf | ||
| ? "--g1000_vcf ${g1000_vcf}" | ||
| : allele_counts_het_snps ? "--allele_counts_het_snps ${allele_counts_het_snps}" : "" |
Member
Author
There was a problem hiding this comment.
To launch the cna part of savana/to, the user needs to provide at least one of the 3 values, but one can only provide one of them for a sample.
Comment on lines
+13
to
+14
| path(contigs) | ||
| path(blacklist) |
Contributor
There was a problem hiding this comment.
Can you add meta maps for these.
Member
Author
There was a problem hiding this comment.
I can, but these inputs are not really varying per-sample, so I left them out on purpose.
Should I still add it? What are the general guidelines for such inputs?
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
This PR adds a new module
savana/to.Because
cnapart ofsavana torequires an adequately large test dataset for copy number fitting @cortés‑ciriano‑lab/savana#110, snapshotting of copy‑number outputs has been deliberately excluded.PR checklist
topic: versions- See version_topicslabelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile conda