rule docker_build:
    input:
        "Dockerfile_momix"
    shell:
        "docker build -t  ejprd/cakut_momix:0.1 -f Dockerfile_momix ."

# 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_all_3methods:
    input:
        "momixRVer.R"
    output:
        "results_momix/cakut_cindex.txt"
    container:
        "docker://ejprd/cakut_momix:0.1"
    params:
        mapped_folder="/data/"
    shell:
        "R -f momixRVer.R --args {params.mapped_folder}, Proteome_common_all.tsv PeptidomeMerged_common_all.tsv, MCIA RGCCA JIVE"
        
