Release 5.1.0 - #468
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genotype and haplotype subflow
…CLONAL_ANALYSIS` subworkflow, feeding its repertoire output into genotype inference.
…e/airrflow into novel-allele-and-genotype
Connect genotyping workflow
…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.
fix skip report error
| error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." | ||
| } | ||
| container "docker.io/immcantation/airrflow:5.0.0" | ||
| container "docker.io/immcantation/airrflow:5.1.0" |
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can we push this container to quay.io/nf-core if the tool can't be put on bioconda?
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Hi Friederike @FriederikeHanssen. I tried to push the container to quay.io/nf-core but failed with unauthorization issue. Could you please tell me how to get authorized to push container to quay.io/nf-core?
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Please raise a request in #request-core on slack and someone from the core team will help you
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Just did it. Hope I can get a feedback soon. Thank you.
| label 'process_long_parallelized' | ||
| label 'immcantation' | ||
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| container "docker.io/immcantation/airrflow:5.1.0" |
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| script: | ||
| """ | ||
| mv "${igblast_dir}" input_igblast_base |
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stageAs might be an alternative that prevents you from copying the data twice in the worst case.
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| if (single_clone_representative) { | ||
| // TODO: Check if we need the cloneby parameter, or here it can be the same as genotypeby. |
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Should this be an issue for follow-up work?
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We solved that internally already, and deleted this comment
FriederikeHanssen
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FriederikeHanssen
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left some comments.
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
atrigila
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atrigila
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I went through the checklist for pipeline releases. Took me a little while to go through all the files, run the code and now I realise some of the comments are similar to what Rike has already mentioned. There are a few warnings in nextflow lint . that you can address if you want to. Same with nf-core pipelines lint, especially those related to the local component structure, which I agree. In any case, this looks good to me :)
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I cannot comment on that file directly but it seems to me that the local UNZIP_DB module could be a process_single instead of a process_medium. Additionally, you might want to consider using the UNZIP nf-core module.
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The same could be done with the GUNZIP module, perhaps you could use the nf-core one and change the arity so that it can process your two R1 and R2 files.
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Some other comments regarding local modules: the samplesheet check (SAMPLESHEET_CHECK) might have been replaced by the checks in schema_input.json, so perhaps this module is no longer necessary?
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Thank you for spotting these, some of these points would take a bit longer to implement and validate, and we're hoping to have a release this week since we want to show some new functionality in a tutorial next week. @Vivian0105 could you open an issue with these points that we will prioritize for next release?
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Yes. I already created several issues to solve in the future based on the reviews
Modify dev based on comments from nf-core reviewers
Check all documentations and make changes based on reviews
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Hi @FriederikeHanssen @atrigila thank you for the reviews! Huimin and I addressed your raised points, but suggest that some of them that will require more implementation and testing to be addressed in the next release, since we are a bit under pressure for releasing this one due to a tutorial and conference next week. I also did not see the nf-core container available yet. Would it be fine to release as is this time, and we prepare a new release with the nf-core container after the tutorial next week? |
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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).