nf-core / nf-core/deepmodeloptim

create toolsheet for preprocessing

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@itrujnara is already working on this.

Since Feb 19, 2025.

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Description

now we have hardcoded:

    ch_preprocessing_config = Channel.of(
        [id:'ZNF367_aliens', variable:'tf_name', target:'ZNF367', background:'LEUTX,ZNF395', background_type:'aliens'],
        [id:'LEUTX_aliens', variable:'tf_name', target:'LEUTX', background:'ZNF367,ZNF395', background_type:'aliens'],
        [id:'ZNF395_aliens', variable:'tf_name', target:'ZNF395', background:'ZNF367,LEUTX', background_type:'aliens']
    )

This is the config input for PREPROCESS_BEDFILE_TO_FASTA

it would be nice to have a toolsheet that handles this:

  1. Get the config needed for a given protocol based on name. so for example, here preprocessing protocol name would be 'preprocess_bedfile_to_fasta'
  2. Parse the corresponding config for the corresponding protocol. So here we would parse all the config needed for PREPROCESS_BEDFILE_TO_FASTA as
    ch_preprocessing_config = Channel.of(
        [id:'ZNF367_aliens', variable:'tf_name', target:'ZNF367', background:'LEUTX,ZNF395', background_type:'aliens'],
        [id:'LEUTX_aliens', variable:'tf_name', target:'LEUTX', background:'ZNF367,ZNF395', background_type:'aliens'],
        [id:'ZNF395_aliens', variable:'tf_name', target:'ZNF395', background:'ZNF367,LEUTX', background_type:'aliens']
    )

I would recommend create a yaml-based toolsheet, because in the future we would have this toolsheet as part of the data_config.

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