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But it fails. This is because the recipes are not in the refgenconf package, so of course it can't provide a list of the requirements from the python interface. When recipes are made flexible, we should keep this in mind.
The text was updated successfully, but these errors were encountered:
yes, there are 2 dedicated properties on Recipe objcts, so you can do this now:
In [9]: rgc = RefGenConf(filepath="r.yaml")
In [10]: bt2_idx_recipe = rgc.get_recipe("bowtie2_index")
In [11]: print(bt2_idx_recipe.requirements)
bowtie2_index recipe requirements:
params:
- threads (Number of threads to use); default: 1
assets:
- fasta (fasta asset for genome); default: fasta
In [12]: bt2_idx_recipe.requirements_table
Out[12]:
bowtie2_index recipe requirements
┏━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━┓
┃ Type ┃ ID ┃ Description ┃ Default value ┃ Argument pattern ┃
┡━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━┩
│ params │ threads │ Number of threads to use │ 1 │ --params threads=1 │
│ assets │ fasta │ fasta asset for genome │ fasta │ --assets fasta=fasta │
└────────┴─────────┴──────────────────────────┴───────────────┴──────────────────────┘
There is no Recipe.requirements_dict though, which would be more elegant, but you can get it this way:
In [4]: bt2_idx_recipe.inputs
Out[4]:
{'files': None,
'params': {'threads': {'description': 'Number of threads to use',
'default': 1}},
'assets': {'fasta': {'asset_class': 'fasta',
'description': 'fasta asset for genome',
'default': 'fasta'}}}
I thought there might be a way to do this:
But it fails. This is because the recipes are not in the refgenconf package, so of course it can't provide a list of the requirements from the python interface. When recipes are made flexible, we should keep this in mind.
The text was updated successfully, but these errors were encountered: