nf-core template merge

[JoseEspinosa]

List of the mains changes that can have an impact for the rest of pipelines developers:

• nextflow schema outdir has not default now
  • The singularity_cache_dir parameter is removed since it is better to have it as an environmental variable, this way shared images between pipelines won't be downloaded twice.
  • The check_max functions is removed as with the new version of nextflow this is no longer needed.
  • The deepmodeloptim is now the only main workflow (under $projectDir/workflows)
  • The previous workflows have been refactored as subworkflows to use the nf-core structure $projectDir/subworkflow/subworkflow_name/main.nf and the dependent code has also been fixed (e.g. includes).

[alessiovignoli]

The stimulus part of the pipeline seems fine to me.