title: running metabat2 with snakemake but not getting the bin files
body: <p>I have been trying to run metabat2 with snakemake. I can run it but the output files in metabat2/ are missing. The checkM that works after it does use the data and can work I just cant find the files later. There should be files created with numbers but it is imposible to predict how many files will be created. Is there a way I can specify it to make sure that the files are created in that file?</p>
  
  <pre><code>rule all:
      [f"metabat2/" for sample in samples],
      [f"checkm/" for sample in samples]
  rule metabat2:
      input:
          "input/consensus.fasta"
      output:
          directory("metabat2/")
      conda:
          "envs/metabat2.yaml"
      shell:
          "metabat2 -i {input} -o {output} -v"
  
  rule checkM:
      input:
          "metabat2/"
      output:
          c = "bacteria/CheckM.txt",
      d = directory("checkm/")
      conda:
          "envs/metabat2.yaml"
      shell:
          "checkm lineage_wf -f {output.c} -t 10 -x fa {input} {output.d}"
  
  </code></pre>
  
  <p>the normal code to run metabat2 would be </p>
  
  <pre><code> metabat2 -i path/to/consensus.fasta -o /outputdir/bin -v 
  </code></pre>
  
  <p>this will create in outputdir files with bin.[number].fa</p>