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include MiXCR toolkit in nf-core/airrflow #346

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include MiXCR toolkit in nf-core/airrflow #346

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mapo9
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@mapo9 mapo9 commented Sep 23, 2024

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

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/airrflow branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Sep 23, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a10a621

+| ✅ 283 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗  12 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 4.1.0
  • pipeline_todos - TODO string in mixcr_exportairr.nf: List required Conda package(s).
  • pipeline_todos - TODO string in mixcr_exportairr.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
  • pipeline_todos - TODO string in mixcr_qc_tags.nf: List required Conda package(s).
  • pipeline_todos - TODO string in mixcr_qc_tags.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
  • pipeline_todos - TODO string in mixcr_qc_chainusage.nf: List required Conda package(s).
  • pipeline_todos - TODO string in mixcr_qc_chainusage.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
  • pipeline_todos - TODO string in mixcr_qc_coverage.nf: List required Conda package(s).
  • pipeline_todos - TODO string in mixcr_qc_coverage.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
  • pipeline_todos - TODO string in mixcr_qc_align.nf: List required Conda package(s).
  • pipeline_todos - TODO string in mixcr_qc_align.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
  • schema_description - Ungrouped param in schema: skip_alignment_filter

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-23 13:35:32

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mapo9 commented Sep 23, 2024

Currently the new mixcr tests fail with
Caused by: Required secret is missing: 'MIXCR_LICENSE'

which is caused by MiXCR requiring a license that is given to the pipeline as a nextflow secret.
I need to figure out how to give the test.config such a secret and ask the MiXCR people if they can provide a license for this cause to make them work.

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@ggabernet ggabernet Awaiting requested review from ggabernet

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