Restructure cwl

runs/kallisto_collect/run.yml

-in_kallisto_results:
-  class: Directory
-  path: ../runs/kallisto/kallisto_results
-in_metadata_file: 
-  class: File
-  path: ../merged_isa_metadata/out/merged_isa.tsv
-in_metadata_sample: "Sample.Name.2"
-in_metadata_factor: "Factor..Photosynthesis.mode."
-out_folder: results