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Sbwf impute glimpse2 #3349

Merged
merged 17 commits into from
May 2, 2023
Merged

Sbwf impute glimpse2 #3349

merged 17 commits into from
May 2, 2023

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LouisLeNezet
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@LouisLeNezet LouisLeNezet commented Apr 28, 2023 •
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PR checklist

PR for new subworkflow for imputation with Glimpse2.
I've also changed some placement mistakes in Glimpse phasing process (1 and 2) and updated the tests concerned accordingly.

  • 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

@LouisLeNezet LouisLeNezet self-assigned this Apr 28, 2023
adamrtalbot
adamrtalbot approved these changes Apr 28, 2023
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Nice, these are tricky modules, well done👍

tests/modules/nf-core/glimpse/concordance/main.nf Outdated Show resolved Hide resolved
modules/nf-core/glimpse/phase/main.nf Show resolved Hide resolved
LouisLeNezet and others added 2 commits May 2, 2023 09:17
@LouisLeNezet @adamrtalbot
Update tests/modules/nf-core/glimpse/concordance/main.nf
e891ad4 
Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
@LouisLeNezet
Merge branch 'master' into sbwf_impute_glimpse2
6e7e16a
@LouisLeNezet LouisLeNezet added this pull request to the merge queue May 2, 2023
@matthdsm
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matthdsm commented May 2, 2023

Nice work 👍🏻 🚀

Merged via the queue into nf-core:master with commit c7ddd48 May 2, 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)
  ...
@LouisLeNezet LouisLeNezet deleted the sbwf_impute_glimpse2 branch July 9, 2024 18:38
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