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Improve preprocessing #419

Merged
merged 26 commits into from
Aug 6, 2021
Merged

Improve preprocessing #419

merged 26 commits into from
Aug 6, 2021

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maxulysse
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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 - add to the software_versions process and a regex to scrape_software_versions.py
    • 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/sarek 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).
  • 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 5, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 181319b

+| ✅ 135 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  12 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version mentioned in Quick Start section.
  • pipeline_todos - TODO string in main.nf: Named file extensions MUST be emitted for ALL output channels
  • pipeline_todos - TODO string in main.nf: List additional required output channels/values here
  • pipeline_todos - TODO string in main.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$ioptions.args" variable
  • pipeline_todos - TODO string in main.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
  • pipeline_todos - TODO string in main.nf: A module file SHOULD only define input and output files as command-line parameters.
  • pipeline_todos - TODO string in main.nf: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.1
  • Run at 2021-08-06 13:47:54

@maxulysse
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Need to merge nf-core/test-datasets#307

@maxulysse maxulysse marked this pull request as ready for review August 6, 2021 13:36
FriederikeHanssen
FriederikeHanssen approved these changes Aug 6, 2021
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@FriederikeHanssen FriederikeHanssen left a comment

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LGTM ❤️

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@maxulysse maxulysse merged commit 6462bc8 into nf-core:dev Aug 6, 2021
@maxulysse maxulysse deleted the dev_bamqc branch August 6, 2021 13:56
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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@maxulysse @FriederikeHanssen