shell.executable("bash")


rule all:
    input:
        "delete_all_output",
        "delete_temp_output",
    output:
        touch("all_ok"),


rule delete_all_output:
    output:
        touch("delete_all_output"),
    shell:
        """
        echo $PATH
        ls
        python -m snakemake --cores 1 -s Snakefile_inner all && \
        rm nothere && \
        python -m snakemake --cores 1 -s Snakefile_inner --dry-run --delete-all-output all && \
        test -f infile && test -f intermediate && test -f some_dir/final && \
        test -d empty_dir && test -L dangling && test -d full_dir
        """


rule delete_temp_output:
    output:
        touch("delete_temp_output"),
    shell:
        """
        python -m snakemake --cores 1 -s Snakefile_inner --notemp temp && \
        python -m snakemake --cores 1 -s Snakefile_inner --dry-run  --delete-temp-output temp && \
        test -f infile && test -f temp_intermediate && \
        test -d temp_empty_dir && test -d temp_full_dir && test -f temp_keep
        """
