Snakefile

configfile: "config.json"

include: "src/snakefiles/datacollect.snakefile"
include: "src/snakefiles/anatomy.snakefile"
include: "src/snakefiles/gene.snakefile"
include: "src/snakefiles/protein.snakefile"
include: "src/snakefiles/geneprotein.snakefile"
include: "src/snakefiles/diseasephenotype.snakefile"
include: "src/snakefiles/process.snakefile"
include: "src/snakefiles/chemical.snakefile"
include: "src/snakefiles/drugchemical.snakefile"
include: "src/snakefiles/taxon.snakefile"
include: "src/snakefiles/genefamily.snakefile"
include: "src/snakefiles/leftover_umls.snakefile"
include: "src/snakefiles/macromolecular_complex.snakefile"
include: "src/snakefiles/publications.snakefile"

include: "src/snakefiles/reports.snakefile"
include: "src/snakefiles/exports.snakefile"

rule all:
    input:
        # See rule all_outputs later in this file for how we generate all the outputs.
        config['output_directory'] + '/reports/outputs_done',
        # reports_done are generated by the rules in src/snakefiles/
        config['output_directory'] + '/reports/reports_done',

        # Build all the exports.
        config['output_directory'] + '/kgx/done',
        config['output_directory'] + '/sapbert-training-data/done',
    output:
        x = config['output_directory'] + '/reports/all_done'
    shell:
        "echo 'done' >> {output.x}"

rule all_outputs:
    input:
        config['output_directory'] + '/reports/anatomy_done',
        config['output_directory'] + '/reports/chemicals_done',
        config['output_directory'] + '/reports/disease_done',
        config['output_directory'] + '/reports/gene_done',
        config['output_directory'] + '/reports/genefamily_done',
        config['output_directory'] + '/reports/geneprotein_done',
        config['output_directory'] + '/reports/process_done',
        config['output_directory'] + '/reports/protein_done',
        config['output_directory'] + '/reports/taxon_done',
        config['output_directory'] + '/reports/umls_done',
        config['output_directory'] + '/reports/macromolecular_complex_done',
        config['output_directory'] + '/reports/drugchemical_done',
        config['output_directory'] + '/reports/publications_done',
    output:
        x = config['output_directory'] + '/reports/outputs_done'
    shell:
        "echo 'done' >> {output.x}"

rule clean_compendia:
    params:
        dir=config['output_directory']
    shell:
        "rm {params.dir}/compendia/*; rm {params.dir}/synonyms/*"

rule clean_downloads:
    params:
        dir=config['download_directory']
    shell:
        "rm -rf {params.dir}/*"