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GOSe-6mo-imputation-paper
GOSe-6mo-imputation-paper
Commit 71f02752 authored by Kevin's avatar Kevin
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...@@ -205,17 +205,18 @@ rule imputation_report: ...@@ -205,17 +205,18 @@ rule imputation_report:
rules.post_process_imputations.output, rules.post_process_imputations.output,
markdown = "reports/imputations.Rmd" markdown = "reports/imputations.Rmd"
output: output:
pdf = "output/{version}/imputations_{model}.pdf", pdf = "output/{version}/gose_imputations_{model}.pdf",
figures = "output/{version}/imputations_{model}_figures.zip" figures = "output/{version}/gose_imputations_{model}_figures.zip"
shell: shell:
""" """
mkdir -p output/{wildcards.version} mkdir -p output/{wildcards.version}
Rscript -e "rmarkdown::render(\\"{input.markdown}\\", output_dir = \\"output/{wildcards.version}\\", params = list(data_dir = \\"../output/{wildcards.version}/data\\", imputations = \\"../output/v1.1/data/imputation/{wildcards.model}/df_gose_imputed.csv\\"))" Rscript -e "rmarkdown::render(\\"{input.markdown}\\", params = list(data_dir = \\"../output/{wildcards.version}/data\\", imputations = \\"../output/v1.1/data/imputation/{wildcards.model}/df_gose_imputed.csv\\"))"
mv reports/imputations.pdf {output.pdf}
mv reports/figures.zip {output.figures} mv reports/figures.zip {output.figures}
""" """
# define corresponding target rule for ease of use # define corresponding target rule for ease of use
rule impute_msm_v1_1: rule impute_msm_v1_1:
input: input:
pdf = "output/v1.1/imputations_msm.pdf", pdf = "output/v1.1/gose_imputations_msm.pdf",
figures = "output/v1.1/imputations_msm_figures.zip" figures = "output/v1.1/gose_imputations_msm_figures.zip"
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