include MiXCR toolkit in nf-core/airrflow#346
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Release 4.1
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Currently the new mixcr tests fail with which is caused by MiXCR requiring a license that is given to the pipeline as a nextflow secret. |
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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: 3.0.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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I adapted the metromap and also added the svg |
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Hi! |
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very much relevant, yes |
ggabernet
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Apr 14, 2025
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Hi @mapo9 thanks for your contributions! I've added some general review comments. The main thing is that as I'm also working on porting modules to nf-core, any new modules should be already part of the nf-core modules if possible. Is it a problem with the mixcr license for the tests?
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Here the diagram indicates that fastp is not run on fastq files when using the MiXCR workflow. Could that be edited so that it is also run or shown as run in the diagram?
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| include { MIXCR_MIXCR } from '../../modules/local/mixcr/mixcr' | ||
| include { MIXCR_MIXCREXPORTAIRR } from '../../modules/local/mixcr/mixcr_exportairr' | ||
| include { MIXCR_MIXCRQCALIGN } from '../../modules/local/mixcr/mixcr_qc_align' | ||
| include { MIXCR_MIXCRQCCOVERAGE } from '../../modules/local/mixcr/mixcr_qc_coverage' | ||
| include { MIXCR_MIXCRQCTAGS } from '../../modules/local/mixcr/mixcr_qc_tags' | ||
| include { MIXCR_MIXCRQCCHAINUSAGE } from '../../modules/local/mixcr/mixcr_qc_chainusage' |
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I'm trying to port all the airrflow modules to nf-core modules, so new processes should be already part of nf-core modules if possible. Is there a reason why this isn't possible?
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This is the example for the sention module which also requires a license file so I think it should be possible, check out this PR: https://github.com/nf-core/modules/pull/8187/files
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I wanted to have the pipeline running first before taking care of the nf-core modules. But you are right, now that it runs we can add them to nf-core
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only problem is that the mixcr people allowed my personal license to be used in the testing as well, but didnt want to give us a testing license. So, at one point when my email is not valid anymore the tests will start failing
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well we can always renew the license when this happens 👍
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| mixcr analyze ${kit} \\ | ||
| --library imgt \\ |
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Would it be possible to allow providing other reference sets? Ideally it should work with the reference data that the user provides as input to the pipeline with the --reference_fasta parameter.
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I think it is possible by providing the library fasta files with the param above and then building the reference file with mixcr buildLibrary (https://mixcr.com/mixcr/guides/create-custom-library/#de-novo-libraries).
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sounds good, I'll add it
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just had a look at the tool. It requires individual fastas for each V, (D), J, (C) region. This is quite different from the input we expect from "reference_fasta" right?
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one could provide the full fasta folder and write the paths here to the individual files. Would that work?
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
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See the MixCR module I'm working on here. Addresses some of the license & CI issues, though with less functionality. Would love to expand the module to include some of the additional workflows included here. I did get a 5 year license from the Milaboratories folks to use for CI testing so that helps, then we'd just need the nf-core folks to add the license as a secret. Happy to help with the development of mixcr into nextflow. |
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Hi I converted this PR to draft due to inactivity, let me know whenever you've done some progress and it is ready for review |
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This PR includes MiXCR preprocessing in the nf-core/airrflow pipelines. It allows to integrate MiXCR preprocessing in the the pipeline, finishing with immcantation postprocessing. MiXCR postprocessing can be performed additionnally as well.
Tests and Docs included
PR checklist
nf-core 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).