Snakefile

rule target:
    input:
        "index.html",
        "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",
        "02-microarray/pathway-analysis_microarray_01_ora.html",
        "02-microarray/pathway-analysis_microarray_02_gsea.html",
        "02-microarray/pathway-analysis_microarray_03_gsva.html",
        "02-microarray/ortholog-mapping_microarray_01_ensembl.html",
        "03-rnaseq/00-intro-to-rnaseq.html",
        "03-rnaseq/clustering_rnaseq_01_heatmap.html",
        "03-rnaseq/differential-expression_rnaseq_01.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",
        "03-rnaseq/ortholog-mapping_rnaseq_01_ensembl.html",
        "03-rnaseq/pathway-analysis_rnaseq_01_ora.html",
        "03-rnaseq/pathway-analysis_rnaseq_02_gsea.html",
        "03-rnaseq/pathway-analysis_rnaseq_03_gsva.html",
        "04-advanced-topics/00-intro-to-advanced-topics.html",
        "04-advanced-topics/network-analysis_rnaseq_01_wgcna.html"


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


rule render_homepage:
    input:
        "components/_homepage.html",
        "components/_navbar.html",
        "components/footer.html",
    output:
        "index.html"
    shell:
        "Rscript scripts/render-homepage.R"