canbind2bids - Snakemake workflow for CAN-BIND raw to bids

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canbind2bids
canbind2bids
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Author: Ali Khan Date: Jan 13, 2022

Run full bids conversion with: 

snakemake -j1 all_unzip && snakemake -j1 all_bids"

Update July 5, 2023 - replaced the DTI data from updated CAN-BIND packages

Code Snippets

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shell: 'unzip -d {output} {input}'
SnakeMake From line 26 of main/Snakefile 
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shell:
    'cp {input} {output}'
SnakeMake From line 46 of main/Snakefile 
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shell:
    '{params.cp_cmd}'
SnakeMake From line 83 of main/Snakefile 
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shell:
    'cp {input} {output}'
SnakeMake From line 91 of main/Snakefile 
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shell:
    'cp {input} {output}'
SnakeMake From line 113 of main/Snakefile 
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run:
    with open(output.json,'w') as jsonfile:
        dd_dict=config['dataset_description']
        for key in dd_dict.keys():
            dd_dict[key] = dd_dict[key].format(**wildcards)
        jsonfile.write(json.dumps(dd_dict, indent=4))
SnakeMake From line 132 of main/Snakefile 
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run:
    with open(output.json,'w') as jsonfile:
        dd_dict=config['bold_json']
        jsonfile.write(json.dumps(dd_dict, indent=4))
SnakeMake From line 142 of main/Snakefile 
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shell: 'unzip -d {output} {input}'
SnakeMake From line 157 of main/Snakefile 
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shell:
    'cp {input}/*/*.csv {output}'
SnakeMake From line 164 of main/Snakefile
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/akhanf/canbind2bids
Name: canbind2bids
Version: 1
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Copyright: Public Domain
License: None
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