Filter array of files to one file

Question

[eduardo]

One step in my workflow produces File[] and I need to filter to grab just one File for the next step. I am trying to use glob without much success. Any hints?

Answer 1

[eduardo]

Michael R. Crusoe point out a couple of solutions:

At workflow level:

in:
  single_file:
    source: other_step/array_of_files
    valueFrom: $(self[0])

[GenoMax]

So this was something already answered by @Michael in one of the other posts? Generally good to link to the original when you do this.

Also accept your answer (green check mark) to provide closure to this question.

[eduardo]

I tried to acknowledge Michael R. Crusoe, but I didn't found a way to link to a specific gitter message. Or were referring to this other post? Converting stdout (File) to string

I made another post because Converting stdout (File) to string was about converting a file to string. The solution is similar.

[eduardo]

valueFrom: $( self.filter(file => !!file.basename.match(/^.*.ids.txt$/)).pop() )

Answer 2

[eduardo]

Add an ExpressionTool step to filter:

cwlVersion: v1.0
class: ExpressionTool

requirements: { InlineJavascriptRequirement: {} }

inputs:
  files:
    type: File[]

expression: |
    ${ return {"ids": inputs.files.filter(file => !!file.basename.match(/^.*\.ids\.txt$/)).pop()}; }

outputs:
  ids:
    type: File