Rename WF dir. Add jinja2 template for input yaml

templates/organisms.yml.j2

+{{ name }}:  # Dummy value to designate the species (isn't used by the script)
+  description:
+  # Species description, leave blank if unknown or you don't want it to be used
+  # These parameters are used to set up the various urls and adresses in different containers
+  # The script requires at least the genus to be specified
+    genus: {{ genus }}  # Mandatory!
+    species: {{ species }} # Mandatory!
+    sex: {{ sex }}
+    strain: {{ strain }}
+    common_name: {{ common_name }}
+    origin: {{ origin }}
+  # the sex and strain, the script will look for files containing the genus, species, sex and strain of the species)
+  # If no file corresponding to the description is found, this path will be considered empty and the script will
+  # proceed to the next step (create the directory tree for the GGA docker stack)
+  data:
+  # Sequence of paths to the different datasets to copy and import into the galaxy container (as a shared library)
+  # Must be absolute paths to the dataset
+    genome_path: {{ genome_path }} # Mandatory!
+    transcripts_path: {{ transcripts_path }}  # Mandatory!
+    proteins_path: {{ proteins_path }} # Mandatory!
+    gff_path: {{ gff_path }} # Mandatory!
+    interpro_path: {{ interpro_path }}
+    orthofinder_path: {{ orthofinder_path }}
+    blastp_path: {{ blastp_path }}
+    blastx_path: {{ blastx_path }}
+    # If the user has several datasets of the same 'nature' (gff, genomes, ...) to upload to galaxy, the next scalar is used by the script to differentiate
+    # between these different versions and name directories according to it and not overwrite the existing data
+    # If left empty, the genome will be considered version "1.0"
+    genome_version: {{ genome_version }}
+    # Same as genome version, but for the OGS analysis
+    ogs_version: {{ ogs_version }}
+    performed_by: {{ performed_by }}
+  services:
+  # Describe what optional services to deploy for the stack
+  # By default, only tripal, tripaldb and galaxy services will be deployed
+    blast: {{ blast }}
+    wiki: {{ wiki }}
+    apollo: {{ apollo }}