Support for Additional Profiles and Clusters #29
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…lusters for reference samples from database parameters
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emarinier
approved these changes
Oct 8, 2024
main.nf
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| if ((params.db_profiles && !params.db_clusters) || (!params.db_profiles && params.db_clusters)) { |
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You don't have to change this, because it's probably easier to understand the way you have it, but you could do this with an XOR: true only if one of the two is true.
I don't think Python (edit: Nextflow/Groovy) has an actual logical XOR operator, so it might reduce to something like:
if bool(params.db_profiles) != bool(params.db_clusters):
but again, just a comment, not necessary to change.
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Great suggestion Eric - played around a bit and got it working here: 7d54942
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It looks good nothing to change. Always have suggestions though! It could be made more clear in the README.md (or with additional error reporting but more work). Basically, it should be emphasized that any address levels in the additional databases that are not in the samplesheet address will be dropped. The error could be triggered if max address size in the samplesheet is smaller than number of columns/levels in the database. As those will be will be dropped (I believe based on how csvtk concat works). For the README.md you could emphasize headers must match and do something like this for the example reference database.
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sgsutcliffe
approved these changes
Oct 8, 2024
apetkau
requested changes
Oct 9, 2024
…laps and loci mismatches with samples from input
…d_profiles and append_clusters functions
…ust be provided together
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Thank you everyone for your review and suggestions! |
apetkau
reviewed
Oct 15, 2024
apetkau
approved these changes
Oct 24, 2024
| # Calculate the frequency of each sample_id across both sources | ||
| csvtk freq -t -f id combined_profiles.tsv > sample_counts.tsv | ||
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| # For any sample_id that appears in both the reference and database, add a 'db_' prefix to the sample_id from the database |
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That's really cool. This would solve the issue with duplicates in all situations then 😄 . Thanks so much.
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| test("Test pipeline when appended profiles or clusters have sample_id overlap") { |
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Thank you for adding this test 😄
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This update aims to enhance the pipeline by integrating additional reference profiles and clusters from user-provided database parameters:
--db_profileswill be incorporated through theAPPEND_PROFILESprocess (which followsLOCIDEX_MERGE_REF).--db_clusterswill be integrated via theAPPEND_CLUSTERSprocess (which followsCLUSTER_FILE).Both parameters are required for their respective processes, and users must provide both; it is not possible to supply only one.
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).