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:
- Get the config needed for a given protocol based on name. so for example, here preprocessing protocol name would be 'preprocess_bedfile_to_fasta'
- Parse the corresponding config for the corresponding protocol. So here we would parse all the config needed for
PREPROCESS_BEDFILE_TO_FASTAas
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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