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dms-vep / dms-vep-pipeline

Pipeline for analyzing deep mutational scanning (DMS) of viral entry proteins (VEPs)
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Periodic Wildcard Error #171

Closed Bernadetadad closed 8 months ago

Bernadetadad commented 8 months ago

@jbloom I'm getting the following wildcard issue when running pipeline on this repo :

Building DAG of jobs...
WorkflowError:
MissingInputException: Missing input files for rule fit_escape:
    output: results/antibody_escape/by_selection/Lib1-240109-cocktail-C952C1596_prob_escape_mean.csv, results/antibody_escape/by_selection/Lib1-240109-cocktail-C952C1596_polyclonal_model.pickle, results/notebooks/fit_escape_antibody_escape_Lib1-240109-cocktail-C952C1596.ipynb
    wildcards: assay=antibody_escape, selection=Lib1-240109-cocktail-C952C1596
    affected files:
        results/spatial_distances/spatial_distances.csv
PeriodicWildcardError: The value _nolegend in wildcard chart is periodically repeated (antibody_escape/averages/cocktail-C952-C1596_mut_effect_nolegend_nolegend_nolegend_nolegend_nolegend_nolegend_nolegend_nolegend_nolegend_nolegend_nolegend_nolegend_nolegend_nolegend_nolegend_nolegend_nolegend_nolegend_nolegend_nolegend). This would lead to an infinite recursion. To avoid this, e.g. restrict the wildcards in this rule to certain values.

Error looks similar to what @fwelsh had in #1 but I tried changing names of this cocktail multiple times and it still leads to the same issue.

jbloom commented 8 months ago

This issue is raised in the wrong repo. It should be in dms-vep-pipeline-3. I am re-raising it there.