rule docker_build:
    input:
        "Dockerfile_wikipathways"
    shell:
        "docker build -t  ejprd/cakut_wikipathways:0.1 -f Dockerfile_wikipathways ."

# Below parameter in params assumes that you map docker with -v parameter a data folder that contains all relevant data
# If this option doesn't work then directly start Docker container from within the shell rule, but then remove the container rule.
rule run_pathway_analysis:
    input:
        "cakut_analysis.R"
    output:
        "output"
    container:
        "docker://ejprd/cakut_wikipathways:0.1"
    params:
        mapped_folder="/data/"
    shell:
        "mkdir multiomics_run && R -f cakut_analysis.R --args {params.mapped_folder}peptide_training_tsv.txt 
        {params.mapped_folder}/peptide_validation_tsv.txt {params.mapped_folder}/peptide_to_protein_tsv.txt 
        {params.mapped_folder}/mirnome_tsv.txt {params.mapped_folder}/proteome_tsv.txt {params.mapped_folder}/wikipathways-20210110-gmt-Homo_sapiens.gmt 
        {params.mapped_folder}/MicroRNA_Target_Sites_curated.csv output"