Array with different flags

CWL Questions
1

Hi everyone,
i have to write a step that have in input an array of file and for each file i need a different prefix. e.g.
bowtie2 -1 *path_file_1* -2 *path_file_2* *other flags*

Are there an elegant way of do it? I found only discussions on array with same prefix. For now i wrote this

baseCommand: [ "bowtie2" ]
arguments:
  - position: 1
    prefix: "-1"
    valueFrom: $(inputs.samples[0])
  - position: 2
    prefix: "-2"
    valueFrom: $(inputs.samples[1])

in: 
  samples: File[]
2

This is basically the same thing, but more compact:

arguments: ["-1", "$(inputs.samples[0])", "-2", "$(inputs.samples[1])"]
3

Does the array only ever have two entries? Then I’d recommend two separate inputs instead of an array. Perhaps the second input is optional

4

The array can have one or two elements and the flags are differents.
When there are two elements the flags are “-1” and “-2”, instead when it only one the flag is “-U”. I think that the usage of inputBinding and prefix is very elegant when the prefix is repeated. I wanted to know if it can do a similar thing but with different prefixes, but I guess not.

Thanks anyway for the replies

5

Perhaps this bowtie2 description in the community repository is sufficient for your needs:

It appears to handle the -U vs -1 & -2 situation.