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Adding and simplifying MaskPrimers options #344

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Adding and simplifying MaskPrimers options #344

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  • also store unproductive seqs
  • make unproductive optional
  • fix cregion primer annotation
  • Merge branch 'dev' of https://github.com/ggabernet/nf-core-airrflow into dev
  • simplify maskprimers score
  • do not save presto intermediate fastq
  • add maskprimers extract option

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 Aug 20, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit b0afe90

+| ✅ 282 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   4 tests had warnings |!
-| ❌   9 tests failed       |-

❌ Test failures:

  • nextflow_config - Default value from the Nextflow schema params.primer_mask_mode = 0.6`` not found in nextflow.config.
  • nextflow_config - Default value from the Nextflow schema params.primer_extract_len = 0.2`` not found in nextflow.config.
  • schema_params - Param primer_r1_mask_mode from nextflow config not found in nextflow_schema.json
  • schema_params - Param primer_r2_mask_mode from nextflow config not found in nextflow_schema.json
  • schema_params - Param maskprimers_extract from nextflow config not found in nextflow_schema.json
  • schema_params - Param primer_r1_extract_len from nextflow config not found in nextflow_schema.json
  • schema_params - Param primer_r2_extract_len from nextflow config not found in nextflow_schema.json
  • schema_params - Default value for param primer_mask_mode invalid: Not in pipeline parameters. Check nextflow.config.
  • schema_params - Default value for param primer_extract_len invalid: Not in pipeline parameters. Check nextflow.config.

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-23 13:40:39

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