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The gcnv contig_ploidy wrapper hardcodes config paths #500

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Nicolai-vKuegelgen opened this issue Apr 15, 2024 · 2 comments · May be fixed by #508
Open

The gcnv contig_ploidy wrapper hardcodes config paths #500

Nicolai-vKuegelgen opened this issue Apr 15, 2024 · 2 comments · May be fixed by #508
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@tedil

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@Nicolai-vKuegelgen
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Describe the bug
The wrapper for gcnv contig_ploidy contains hard-coded config sections (see below) but is uactually sed by different steps (helper_gcnv_model_targeted and helper_gcnv_model_wgs)

From snappy_wrappers/wrappers/gcnv/contig_ploidy/wrapper.py

par_intervals = snakemake.config["step_config"]["helper_gcnv_model_targeted"]["gcnv"].get(
    "path_par_intervals"
)

To Reproduce
Steps to reproduce the behavior:

  1. Run the helper_gcnv_model_wgs step

Expected behavior
The wrapper script should automatically determine whether the targeted or wgs step is being run.
@tedil
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tedil commented Apr 30, 2024

The wrapper should not determine anything but remain oblivious of its context. I'd rather factor the config access out and make the par_intervals a parameter, i.e. an entry in params.args. I.e. the steps calling this wrapper should be in charge of producing the correct par_intervals value to hand off to the wrapper.

@tedil tedil self-assigned this Apr 30, 2024
@Nicolai-vKuegelgen
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Sounds like a better solution, I have so far only 'hotfixed' this by adding a "helper_gcnv_model_targeted" config section to my WGS projects.

@tedil tedil linked a pull request Apr 30, 2024 that will close this issue
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@tedil tedil

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fix: move config access in gcnv/contig_ploidy wrapper to params bihealth/snappy-pipeline
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@tedil @Nicolai-vKuegelgen