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Add Vizgenpostprocessing/preparesegmentation module #8575
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Add Vizgenpostprocessing/preparesegmentation module #8575
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Thanks for your contribution.
There is a few modification to make it more nf-core like.
modules/nf-core/vizgenpostprocessing/preparesegmentation/main.nf
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modules/nf-core/vizgenpostprocessing/preparesegmentation/meta.yml
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Co-authored-by: Louis Le Nézet <[email protected]>
…/main.nf.test Co-authored-by: Louis Le Nézet <[email protected]>
Co-authored-by: Louis Le Nézet <[email protected]>
Thanks you @LouisLeNezet for the review! I've implemented your suggestions. I am getting CI fails now due to an unrelated module. Do you have any suggestions here? |
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Thanks for fixing the modules, this is much better !
Just a few comments before merging.
For the CI fail, something bad migth have happen in another PR.
We will look into it.
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Co-authored-by: Louis Le Nézet <[email protected]>
Co-authored-by: Louis Le Nézet <[email protected]>
Hi @mcmero could you set the prefix as mentioned ? |
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Ready to go when the test pass !
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Could you fix the two alignment ? |
Co-authored-by: Louis Le Nézet <[email protected]>
Co-authored-by: Louis Le Nézet <[email protected]>
@mcmero Could you check that your branch is correctly in sync with the master branch. |
PR checklist
Closes #8441
versions.yml
file.label
nf-core modules test <MODULE> --profile docker
nf-core modules test <MODULE> --profile singularity
nf-core modules test <MODULE> --profile conda
nf-core subworkflows test <SUBWORKFLOW> --profile docker
nf-core subworkflows test <SUBWORKFLOW> --profile singularity
nf-core subworkflows test <SUBWORKFLOW> --profile conda
This PR adds the
preparesegmentation
process for cell segmentation using the vizgen-postprocessing tool for the MERSCOPE spatial omics instrument. The plan would be to addrunsegmentationontile
andcompiletilesegmentation
as subsequent modules to create a segmentation subworkflow for the tool.The test data is prepared within the test module, using generated dummy data plus an existing segmentation image in
nf-core/test-datasets
, which needs to be renamed and put in an images directory to work with this module.I could not find a BioContainer or BioConda package for this tool.