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Default deconvolution config is missing #161

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GeertvanGeest opened this issue Sep 13, 2024 · 0 comments
Open

Default deconvolution config is missing #161

GeertvanGeest opened this issue Sep 13, 2024 · 0 comments

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@GeertvanGeest
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GeertvanGeest commented Sep 13, 2024

Describe the bug
The default for deconvolution.deconvolution_config is "{VPIPE_BASEDIR}/../resources/cowwid/deconv_linear_logit_quasi_strat.yaml". However, this file does not exist in the repository (at least not in the default branch).

This results in the following error if no deconvolution config is specified:

MissingInputException in rule deconvolution in file /Users/geertvangeest/Documents/repositories/test-vpipe/vp-analysis/V-pipe/workflow/rules/signatures.smk, line 309:
Missing input files for rule deconvolution:
    output: results/deconvoluted.tsv.zst, results/deconvoluted_upload.json
    affected files:
        /Users/geertvangeest/Documents/repositories/test-vpipe/vp-analysis/V-pipe/workflow/../resources/cowwid/deconv_linear_logit_quasi_strat.yaml

To Reproduce

config.yaml:

general:
    virus_base_config: 'sars-cov-2'

input:
    samples_file: samples.tsv
    variants_def_directory: vocs/

output:
    samples_file: samples.tsv
    trim_primers: true

tallymut: 
    timeline_file: timeline.tsv

V-pipe command:

./vpipe --cores 8 deconvolution

Expected behavior
The pipeline runs without failure

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