refinebio-examples/Snakefile at master · Riyan-Rickson/refinebio-examples · GitHub

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rule target:
    input:
        "01-getting-started/getting-started.html",
        "02-microarray/00-intro-to-microarray.html",
        "02-microarray/differential-expression_microarray_01_2-groups.html",
        "02-microarray/differential-expression_microarray_02_several-groups.html",
        "02-microarray/clustering_microarray_01_heatmap.html",
        "02-microarray/dimension-reduction_microarray_01_pca.html",
        "02-microarray/dimension-reduction_microarray_02_umap.html",
        "02-microarray/gene-id-annotation_microarray_01_ensembl.html",
        "03-rnaseq/clustering_rnaseq_01_heatmap.html",
        "03-rnaseq/differential-expression_rnaseq_01.html",
        "03-rnaseq/00-intro-to-rnaseq.html",
        "03-rnaseq/dimension-reduction_rnaseq_01_pca.html",
        "03-rnaseq/dimension-reduction_rnaseq_02_umap.html",
        "03-rnaseq/gene-id-annotation_rnaseq_01_ensembl.html",
        "04-advanced-topics/00-intro-to-advanced-topics.html"

rule render_citations:
    input:
        rmd = "{basedir}/{basename}.Rmd",
        nav = "{basedir}/_navbar.html",
        bib = "references.bib",
        csl = "components/genetics.csl"
    output:
       "{basedir}/{basename}.html"
    shell:
        "Rscript scripts/render-notebooks.R"
        " --rmd {input.rmd}"
        " --bib_file {input.bib}"
        " --cite_style {input.csl}"
        " --html {output}"
        " --style"