
rule:
    name: "foo_rule"
    message: "Running foo_step implementation: foo_imp"
    input:
        dummy_container_main_input_file_paths=['some/path/to/input_chunks/{chunk}/quux'],
        dummy_container_secondary_input_file_paths=['bar'],
    output: ['some/path/to/processed/{chunk}/quux']
    log: "spam/foo_rule-output-{chunk}.log"
    container: "Multipolarity.sif"
    shell:
        '''
        export DUMMY_CONTAINER_OUTPUT_PATHS=some/path/to/processed/{wildcards.chunk}/quux
        export DUMMY_CONTAINER_DIAGNOSTICS_DIRECTORY=spam
        export DUMMY_CONTAINER_MAIN_INPUT_FILE_PATHS=some/path/to/input_chunks/{wildcards.chunk}/quux
        export DUMMY_CONTAINER_SECONDARY_INPUT_FILE_PATHS=bar
        export eggs=coconut
        echo hello world > {log} 2>&1
        '''