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Cellbender empty droplet removal #7031

Merged
merged 11 commits into from
Dec 3, 2024
Merged

Cellbender empty droplet removal #7031

merged 11 commits into from
Dec 3, 2024

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chaochaowong
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@chaochaowong chaochaowong commented Nov 19, 2024 •
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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

@chaochaowong chaochaowong assigned chaochaowong and unassigned SPPearce and nictru Nov 26, 2024
@chaochaowong
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chaochaowong commented Nov 26, 2024 •
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Hi, @SPPearce, Thank you for your suggestions. I have incorporated them into the PR. Last week there were some unrelated CI problems and then some PR run Linting hiccups. Now all checks have passed, and it is ready to be reviewed and to merge. Thank you.

@chaochaowong
rename subworkflow name to
7efdabf 
H5AD_REMOVEBACKGROUND_BARCODES_CELLBENDER_ANNDATA from  CELLBENDER_EMPTY_DROPLET_REMOVAL
@chaochaowong
Merge branch 'master' into cellbender_empty_droplet_removal
9ad8cbd 
merge to update master
@SPPearce
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SPPearce commented Dec 3, 2024

Feel free to hit the merge button if you are happy.

@chaochaowong chaochaowong added this pull request to the merge queue Dec 3, 2024
Merged via the queue into nf-core:master with commit 23600f6 Dec 3, 2024
22 checks passed
@chaochaowong chaochaowong deleted the cellbender_empty_droplet_removal branch December 3, 2024 21:21
LouisLeNezet pushed a commit to LouisLeNezet/modules that referenced this pull request Dec 4, 2024
@chaochaowong
Cellbender empty droplet removal (nf-core#7031)
ae0430b 
* add cellbender_empty_droplet_removal subworkflow

* correct the path to cellbender and anndata nf-core modules

* edit description of the output

* edited test for subworkflow cellbender_empty_droplet_removal

* add test snapshot (sigularity) for cellbender_empty_droplot_removal
subworkflows

* edited meta.yml to pass nf-core subworkflows lint

* updated to remove ch_h5ad and just emit h5ad=ANNDATA_BARCODES.out.h5ad

* rename subworkflow name to
H5AD_REMOVEBACKGROUND_BARCODES_CELLBENDER_ANNDATA from  CELLBENDER_EMPTY_DROPLET_REMOVAL
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@SPPearce SPPearce SPPearce approved these changes

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@chaochaowong @SPPearce @nictru