feat: enabled mbcs meta-tool in the ngs_mapping step model #545
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The pull request CI testing is failing due to mamba configuration. It seems to use miniconda instead of miniforge, and it seems that the new conda solver matches mamba's performance(?). |
| @@ -28,6 +28,6 @@ class HlaTyping(SnappyStepModel, validators.ToolsMixin, validators.NgsMappingMix | |||
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| tools: Annotated[list[Tool], EnumField(Tool, [Tool.optitype], min_length=1)] | |||
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| optitype: Optitype | None = None | |||
| optitype: Optitype = Optitype() | |||
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Before I forget: This is a design decision we must make.
- Either we always provide all the defaults, and substeps are always registered irrespective of whether they're used or not, or
- we do not provide defaults but force
None, in which case substeps must not be registered if the config doesn't provide the substeps and all functions in the workflow definitions (in the init.py files) must not access those non-existent config definitions (e.g. intget_output_filesetc).
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I am tempted to always provide defaults. It makes the __init__.py code easier, and I personally don't like to see:
step_config:
hla_typing:
tools: [optitype]
optitype: {}
For me, the syntax optitype: {} suggests that the tool doesn't accept parameters, not that we use the defaults.
Also, I wouldn't always set all defaults for more complex steps/tools. If there isn't an obvious choice for a default, then the user should make a decision.
But again, I am prepared to be convinced otherwise.
| if self.name not in self.config.tools: | ||
| return {} |
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This also touches on the comment above
| @@ -53,7 +53,7 @@ def pair_fastq_files(input_left, input_right): | |||
| input_left = snakemake.params.args["input"]["reads_left"] | |||
| input_right = snakemake.params.args["input"].get("reads_right", "") | |||
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| config = snakemake.config["step_config"]["ngs_mapping"]["somatic"] | |||
| config = snakemake.config["step_config"]["ngs_mapping"]["mbcs"] | |||
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for now, we can do it like this, and then later move those config accesses to the parameters
Quick & dirty fix.
TODO: check & fix the whole pipeline (#528 )