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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
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:
To Reproduce
config.yaml:
V-pipe command:
Expected behavior
The pipeline runs without failure
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