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Fixing failing subworkflow tests #3343

Merged
merged 10 commits into from
Apr 28, 2023
Merged

Fixing failing subworkflow tests #3343

merged 10 commits into from
Apr 28, 2023

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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:
    • PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

@maxulysse maxulysse mentioned this pull request Apr 27, 2023
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@maxulysse
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conda is failing with fastq_align_dna as usual

@maxulysse maxulysse added this pull request to the merge queue Apr 28, 2023
Merged via the queue into nf-core:master with commit 5c3a343 Apr 28, 2023
jvfe added a commit to jvfe/modules that referenced this pull request May 2, 2023
@jvfe
Merge branch 'master' into islandpath
95cb7c8 
* master: (97 commits)
  Use long form docker.io address for Ubuntu (nf-core#3358)
  Default registry to quay.io (nf-core#3344)
  Sbwf impute glimpse2 (nf-core#3349)
  added cellranger vdj/mkvdjref modules, with module test for vdj (nf-core#3033)
  Add space to fix singularity download error on shinyngs modules (nf-core#3351)
  Output channel modification star (nf-core#3350)
  fix corrected typo in output (nf-core#3337)
  give execution permissions to dumpsoftwareversions.py (nf-core#3347)
  fix meta.ymls for dumpsoftware and multiqc (nf-core#3345)
  Fixing failing subworkflow tests (nf-core#3343)
  remove imputeme module since it is evidently no longer supported (nf-core#3223)
  Update path for yaml-schema json (nf-core#3340)
  New module MetaPhlAn4 (nf-core#3298)
  Update ALL bcftools modules (nf-core#3339)
  update docker and singularity version of p7zip (nf-core#3338)
  update sratools/fasterqdump to handle 10X data (nf-core#3336)
  Make MAD plots optional in shinyngs (nf-core#3334)
  reset tools in CI to released version (nf-core#3335)
  new module wisecondorx/gender (nf-core#3333)
  Bump shinyngs modules (nf-core#3323)
  ...
jvfe added a commit to jvfe/modules that referenced this pull request May 2, 2023
@jvfe
Merge branch 'master' into update-panaroo/run
0e077da 
* master: (120 commits)
  Use long form docker.io address for Ubuntu (nf-core#3358)
  Default registry to quay.io (nf-core#3344)
  Sbwf impute glimpse2 (nf-core#3349)
  added cellranger vdj/mkvdjref modules, with module test for vdj (nf-core#3033)
  Add space to fix singularity download error on shinyngs modules (nf-core#3351)
  Output channel modification star (nf-core#3350)
  fix corrected typo in output (nf-core#3337)
  give execution permissions to dumpsoftwareversions.py (nf-core#3347)
  fix meta.ymls for dumpsoftware and multiqc (nf-core#3345)
  Fixing failing subworkflow tests (nf-core#3343)
  remove imputeme module since it is evidently no longer supported (nf-core#3223)
  Update path for yaml-schema json (nf-core#3340)
  New module MetaPhlAn4 (nf-core#3298)
  Update ALL bcftools modules (nf-core#3339)
  update docker and singularity version of p7zip (nf-core#3338)
  update sratools/fasterqdump to handle 10X data (nf-core#3336)
  Make MAD plots optional in shinyngs (nf-core#3334)
  reset tools in CI to released version (nf-core#3335)
  new module wisecondorx/gender (nf-core#3333)
  Bump shinyngs modules (nf-core#3323)
  ...
@maxulysse maxulysse deleted the subworkflow-tests-fix branch November 23, 2023 13:24
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@mashehu mashehu mashehu approved these changes

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@maxulysse @mashehu