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Avoiding clashes of config of FILTERVARIANTTRANCHES in different subworkflows #1315

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merged 4 commits into from
Nov 7, 2023
Merged

Avoiding clashes of config of FILTERVARIANTTRANCHES in different subworkflows #1315

merged 4 commits into from
Nov 7, 2023

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asp8200
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@asp8200 asp8200 commented Nov 7, 2023

Hopefully fixing #1314

TO-DO: Update changelog

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/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 --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 Nov 7, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a68a92f

+| ✅ 144 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowSarek.groovy: Optionally add in-text citation tools to this list.
  • schema_description - No description provided in schema for parameter: bcftools_annotations
  • schema_description - No description provided in schema for parameter: bcftools_annotations_index
  • schema_description - No description provided in schema for parameter: bcftools_header_lines

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-07 15:08:16

@asp8200 asp8200 changed the title Avoiding classes of config of FILTERVARIANTTRANCHES in different subworkflows Avoiding clashes of config of FILTERVARIANTTRANCHES in different subworkflows Nov 7, 2023
maxulysse
maxulysse approved these changes Nov 7, 2023
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LGTM

FriederikeHanssen
FriederikeHanssen requested changes Nov 7, 2023
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Changelog update

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asp8200 commented Nov 7, 2023

Changelog update

Yeah, I know. I even wrote it in the description of the PR ;-)

@FriederikeHanssen FriederikeHanssen marked this pull request as ready for review November 7, 2023 19:21
@FriederikeHanssen FriederikeHanssen merged commit dc9717a into dev Nov 7, 2023
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@asp8200 asp8200 deleted the fix_1314 branch November 11, 2023 11:55
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@maxulysse maxulysse maxulysse approved these changes

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@asp8200 @maxulysse @FriederikeHanssen