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remove params.outdir from modules and subworfklows tests #5007

Merged
merged 10 commits into from
Feb 28, 2024
Merged

remove params.outdir from modules and subworfklows tests #5007

merged 10 commits into from
Feb 28, 2024

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maxulysse
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PR checklist

Closes #XXX

  • 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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@maxulysse maxulysse marked this pull request as ready for review February 28, 2024 12:21
@maxulysse maxulysse requested a review from a team as a code owner February 28, 2024 12:54
@maxulysse maxulysse mentioned this pull request Feb 28, 2024
Merged
3 tasks
@maxulysse maxulysse added this pull request to the merge queue Feb 28, 2024
@github-merge-queue github-merge-queue bot removed this pull request from the merge queue due to failed status checks Feb 28, 2024
@maxulysse maxulysse added this pull request to the merge queue Feb 28, 2024
@github-merge-queue github-merge-queue bot removed this pull request from the merge queue due to failed status checks Feb 28, 2024
@drpatelh drpatelh merged commit 5caf764 into nf-core:master Feb 28, 2024
71 of 76 checks passed
jch-13 pushed a commit to jch-13/modules that referenced this pull request Mar 19, 2024
@maxulysse @jch-13
remove params.outdir from modules and subworfklows tests (nf-core#5007)
8a3da1a 
* remove params.outdir from modules and subworfklows tests

* update usage of params outdir

* update more tests

* Apply suggestions from code review

* Apply suggestions from code review

* update snap

* update snap

* update even more snaps

* remove obsolete snaps
jennylsmith pushed a commit to RSC-RP/modules that referenced this pull request Mar 20, 2024
@maxulysse @jennylsmith
remove params.outdir from modules and subworfklows tests (nf-core#5007)
2d40f21 
* remove params.outdir from modules and subworfklows tests

* update usage of params outdir

* update more tests

* Apply suggestions from code review

* Apply suggestions from code review

* update snap

* update snap

* update even more snaps

* remove obsolete snaps
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@sateeshperi sateeshperi sateeshperi approved these changes

@adamrtalbot adamrtalbot Awaiting requested review from adamrtalbot

@drpatelh drpatelh Awaiting requested review from drpatelh

@Midnighter Midnighter Awaiting requested review from Midnighter

@JoseEspinosa JoseEspinosa Awaiting requested review from JoseEspinosa

@matthdsm matthdsm Awaiting requested review from matthdsm

@jfy133 jfy133 Awaiting requested review from jfy133

@luisas luisas Awaiting requested review from luisas

@GCJMackenzie GCJMackenzie Awaiting requested review from GCJMackenzie

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3 participants
@maxulysse @sateeshperi @drpatelh