Include modules bin folder

[JoseEspinosa]

The path to the binaries of the included modules is not automatically loaded as it is in the case of the main workflow. By the moment this is not implemented in Nextflow so this can only be solved using workarounds:

• The simplest one will be to check for bin folders inside the pipeline and the benchmarker path and through a warning if they are detected advising to copy the main workflow bin.

• Add the following snippet to the main nextflow.config file:

  modulesPipelineBin = "$PATH:${params.pipeline_path}/bin"
  
  env {
       PATH = modulesPipelineBin
  }
  

  This approach has the caveat that if containers are being used, then the PATH environmental variable of the container is overwritten. To solve this, the path of the container could be also provided in the same snippet, so for instance in the case of a t_coffee container that has the t_coffee binaries in /opt/tcoffee/bin the first line of the previous snippet can be changed to:
  modulesPipelineBin = "$PATH:${params.pipeline_path}/bin:/opt/tcoffee/bin"

• Another option is to create a profile named bin which contains the snipped above.