add functional annotation directory to create-symlink.cwl

[mpoelchau]

Most of our new organisms should now have functional annotations. We need to incorporate them into the create-symlink.cwl workflow, based on the functional annotation directory name. I think the steps to add this should look something like this:

• Add functional annotation directory name to yml file; perhaps to the tree input?
• It would be great if this step could be conditional - perhaps based on whether the functional annotation directory name is NA or not?
• I suspect the command inside the workflow will look something like this:

• baseCommand: [ln]
  arguments:
  - prefix: -s
  position: 1
  valueFrom: $(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/$(inputs.deepPATH_analyses[0])/[functional-annotation-directory-name]/
  #target directory
  - position: 5
  valueFrom: $(inputs.MAIN_PATH)/$(inputs.tree[0])-($(inputs.scientific_name[0])_$(inputs.scientific_name[1]))/$(inputs.tree[1])/2.Official or Primary Gene Set/.

[mpoelchau]

Btw, the above example code snippet is derived from https://github.com/NAL-i5K/Organism_Onboarding/blob/master/flow_reorganize_symlinks/analyses_symlink.cwl

[mpoelchau]

Added in #140