How to output a file ?

[dridk]

I don't know how to specify the output filename ! Using type = local_file create a file output inside the output folder. But I want a file named "merged.vcf" .

workflow:
    steps:
      - name: Step1 
        cmd: /bin/bash run.sh $input > $output
        bash: true

    inputs:
      - id: input
        description: a zip folder with many VCF 
        type: local_file

    outputs:
      - id: output
        description: Merged vcf file 
        type: local_file

[alisongonpereira]

I don't know if you still trying with cloudgene, but a workaround would be do define a output folder and write your files there with a custom input name (you are gonna need a new variable in the input. Would be something like:

workflow:
steps:
- name: Step1
cmd: /bin/bash run.sh $input > "${output}/${filePrefix}.merged.vcf.gz"
bash: true

inputs:
  - id: input
    description: a zip folder with many VCF 
    type: local_file

  - id: filePrefix
    description: name your output
    type: text

outputs:
  - id: output
    description: Merged vcf folder
    type: local_folder

Maybe this works? My knowledge of where the "{" goes is kinda limited