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Try to fix RRA #214

Merged
merged 12 commits into from
Nov 8, 2024
Merged

Try to fix RRA #214

merged 12 commits into from
Nov 8, 2024

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LaurenceKuhl
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@LaurenceKuhl LaurenceKuhl commented Oct 29, 2024 •
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This PR is to add singularity and docker tests to our pipeline and also fix certain issues users were experience when running hte pipeline with docker or singularity, especially with the MAGECKFlute package

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github-actions bot commented Oct 29, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 957b5f2

+| ✅ 240 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.3.0
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_exist - File is ignored: conf/test.config
  • files_exist - File is ignored: conf/test_full.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-11-08 09:22:51

jfy133
jfy133 reviewed Nov 8, 2024
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.github/workflows/ci.yml Outdated
@@ -41,7 +41,7 @@ jobs:
- "test_umis"
- "test_screening_count_table"
isMaster:
- ${{ github.base_ref == 'master' }}
- true
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Are you sure you want this to always run? That seems sort of overkill in terms of the polarbears (this would be every single CI run you will run 3 profiles x 6 tests x 2 nextflow version everytime...?

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no you're right i think we wanted to just run it for this PR, let me modify it

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I would suggest to test singularity manually by opening a draft PR against master (just don't merge it)

LaurenceKuhl
LaurenceKuhl commented Nov 8, 2024
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.github/workflows/ci.yml Outdated Show resolved Hide resolved
@LaurenceKuhl LaurenceKuhl merged commit be6922e into nf-core:dev Nov 8, 2024
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@jfy133 jfy133 jfy133 left review comments

@sateeshperi sateeshperi sateeshperi approved these changes

@mashehu mashehu Awaiting requested review from mashehu

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5 participants
@LaurenceKuhl @jfy133 @sateeshperi @mirpedrol @medmaca