Species metabolic coupling analysis with SMETANA

Now we organize our GEMs into sample specific folders prior to simulation using organizeGEMs:

rule organizeGEMs:
    input:
        f'{config["path"]["root"]}/{config["folder"]["refined"]}'
    message:
        """
        Organizes GEMs into sample specific subfolders, assumes that the refined_bins folder has sample-specific subfolders. 
        Necessary to run smetana per sample using the IDs wildcard.
        """
    shell:
        """
        cd {input}
        for folder in */;do
            echo -n "Creating GEM subfolder for sample $folder ... "
            mkdir -p ../{config[folder][GEMs]}/$folder;
            echo -n "moving GEMs ... "
            mv ../{config[folder][GEMs]}/$(echo $folder|sed 's|/||')_*.xml ../{config[folder][GEMs]}/$folder;
            echo "done. "
        done
        """

Now we switch back to using the wildcard expansion of sample specific {{IDs}} to run SMETANA simulations per sample:

rule smetana:
    input:
        f'{config["path"]["root"]}/{config["folder"]["GEMs"]}/{{IDs}}'
    output:
        f'{config["path"]["root"]}/{config["folder"]["SMETANA"]}/{{IDs}}_detailed.tsv'
    benchmark:
        f'{config["path"]["root"]}/benchmarks/{{IDs}}.smetana.benchmark.txt'
    shell:
        """
        set +u;source activate {config[envs][metabagpipes]};set -u
        mkdir -p {config[path][root]}/{config[folder][SMETANA]}
        cp {config[path][root]}/{config[folder][scripts]}/{config[scripts][carveme]} {input}/*.xml $SCRATCHDIR
        cd $SCRATCHDIR
        
        smetana -o $(basename {input}) --flavor fbc2 \
            --mediadb media_db.tsv -m {config[params][smetanaMedia]} \
            --detailed \
            --solver {config[params][smetanaSolver]} -v *.xml
        
        cp *.tsv {config[path][root]} #safety measure for backup of results in case rule fails for some reason
        mv *.tsv $(dirname {output})
        """