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CHORES: update all modules #1304

Merged
merged 21 commits into from
Nov 3, 2023
Merged

CHORES: update all modules #1304

merged 21 commits into from
Nov 3, 2023

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maxulysse
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update all modules (will probably break things)

@maxulysse maxulysse marked this pull request as draft November 1, 2023 14:41
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github-actions bot commented Nov 1, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 202ebd9

+| ✅ 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 2023-11-03 09:29:26

@maxulysse maxulysse marked this pull request as ready for review November 1, 2023 19:09
@maxulysse maxulysse changed the title CHORES: WIP update all modules CHORES: update all modules Nov 1, 2023
@maxulysse
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All the comments should be transferred as issue in modules

@maxulysse
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failed tests are:

  • nf-test tests for modules that need data but it'll be fixed in a separate PR.
  • sentieon tests (but the modules and subworkflows haven't changed, so we should be ok), and we will retrigger them anyway

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Something looks wrong with the gatk4spark tests, I'll look into it tomorrow

FriederikeHanssen
FriederikeHanssen reviewed Nov 2, 2023
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🤯 some small things we should clear up before merging. But looks super good

modules/nf-core/bwa/mem/environment.yml Show resolved Hide resolved
modules/nf-core/bwamem2/mem/environment.yml Show resolved Hide resolved
modules/nf-core/deepvariant/environment.yml Show resolved Hide resolved
modules/nf-core/dragmap/align/environment.yml Show resolved Hide resolved
modules/nf-core/gatk4/cnnscorevariants/environment.yml Show resolved Hide resolved
modules/nf-core/manta/tumoronly/main.nf Show resolved Hide resolved
modules/nf-core/manta/somatic/main.nf Show resolved Hide resolved
modules/nf-core/manta/germline/main.nf Show resolved Hide resolved
modules/nf-core/cnvkit/batch/main.nf Show resolved Hide resolved
modules/nf-core/bcftools/mpileup/main.nf Show resolved Hide resolved
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FriederikeHanssen
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sorry aparently some files weren't loaded last night. taking back everything about channel magic

subworkflows/local/bam_variant_calling_germline_all/main.nf Show resolved Hide resolved
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FriederikeHanssen
FriederikeHanssen approved these changes Nov 3, 2023
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only sentieon is failing, everything is else is it's own issue now

@maxulysse maxulysse merged commit d6a1230 into nf-core:dev Nov 3, 2023
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@maxulysse maxulysse deleted the modules branch November 3, 2023 12:11
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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@maxulysse @FriederikeHanssen