Novel allele and genotype#443
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…CLONAL_ANALYSIS` subworkflow, feeding its repertoire output into genotype inference.
…to novel-allele-and-genotype
… handling arguments.
…ENOTYPING` subworkflow.
…teps, and update `enchantr`'s `outputby` parameter to `cloneby`.
…AND_GENOTYPE` and update its conditional execution logic.
…yping is enabled and add `skip_clonal_analysis` to test configuration.
…ES_AND_GENOTYPING`.
…NOTYPING process.
… `repertoire` output channel name to `repertoires` in `novel_alleles_and_genotyping`.
…g samplesheet collection and update test configurations.
…l allele and Bayesian genotype inference modules.
… `db_novel` to `*_report`.
…ata and adjust `novel_alleles_and_genotyping` subworkflow data flow accordingly.
…tsv` to `reassign-pass.tsv`.
… perform clonal analysis before Bayesian genotype inference and correct a log file path.
…e` to use `species='auto'` and fix log output path for the latter.
ggabernet
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ggabernet
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I have some comments but otherwise looks good to me!
| // infer clones (gets the reference from novel alleles inference in any case) | ||
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| if (params.single_clone_representative) { | ||
| CLONAL_ANALYSIS( |
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This is ok for now if i works, however we'll change this and use here only the process that actually infers clones.
There is also a process missing (probably a separate enchantR report again that selects one representative per clone. Or we could update the existing clonal inference notebook to add an optional param to select one representative per clone so it doesn't need a separate Rmd script.
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the one representative per clone is within the genotype inference report. If the user want to use all the sequences regardless of the clones, then there is no need to infer them at all.
| ch_validated_samplesheet.collect() | ||
| ch_for_genotyping, | ||
| ch_for_reference, | ||
| [] |
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If this is not needed can the input channel be removed from the process?
| REASSIGN_ALLELES_NOVEL ( | ||
| ch_grouped_repertoires, | ||
| NOVEL_ALLELE_INFERENCE.out.reference, | ||
| [], |
| NOVEL_ALLELE_INFERENCE ( | ||
| ch_grouped_repertoires, | ||
| ch_reference_fasta, | ||
| [] |
| BAYESIAN_GENOTYPE_INFERENCE.out.reference, | ||
| ch_validated_samplesheet.collect(), | ||
| "segments" //TODO: update this to pass actual segments. | ||
| [], |
… parameter and remove `repertoires_samplesheet` input from enchantr modules.
…NAL_ASSIGNMENT_COMPUTE`.
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.5.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
…nce FASTA within the main data tuple and introduce an `outputby` parameter for allele reassignment.
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Great, thank you @ayeletperes I'll be merging this PR and we can continue the development in follow-up PRs. |
ggabernet
merged commit 0ed5dde
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nf-core:novel-allele-and-genotype
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,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).