First complet version of the workflow with snakemake

public 1yr ago Version: v1.0.0 0 bookmarks

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BGNN_Snakemake

First complete version of the BGNN image segmentation workflow managed using snakemake.

1- Introduction

The image segmentation workflow is managed using snakemake, a user-friendly python workflow manager. Snakemak

Code Snippets

shell: 'wget -O {output} {params.download_link} > {log} 2>&1'

SnakeMake From line 16 of workflow/Snakefile

shell: 'gen_metadata.py {input} --device cpu --outfname {output.metadata} --maskfname {output.mask} > {log} 2>&1'

SnakeMake From line 27 of workflow/Snakefile

shell: 'python /pipeline/dm_formatter.py {input} {output} > {log} 2>&1'

SnakeMake From line 36 of workflow/Snakefile

shell: 'Crop_image_main.py {input.image} {input.metadata} {output} > {log} 2>&1'

SnakeMake From line 47 of workflow/Snakefile

shell:
    'segmentation_main_rescale_origin.py {input} {output} > {log} 2>&1'

SnakeMake From line 56 of workflow/Snakefile

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Created: 1yr ago

Updated: 1yr ago

Maitainers: public

URL: https://github.com/hdr-bgnn/BGNN_Core_Workflow

Name: bgnn_core_workflow

Version: v1.0.0

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License: MIT License

Keywords:

Image Expression analysis Ontology metadata segmentation-fold Snakemake morphology analysis

Future updates

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