Translation for array of array of file

[junyk]

For some Bioinformatics tool, we may want to pass more than one pair of FASTQ files.
In Janis, it is declared like this:

ToolInput(
    "readFilesIn",
    Array(FastqGzPair(optional=True)),
    prefix="--readFilesIn"
)

In wdl, this input was translated into:

 Array[Array[File]] reads

The command argument looked like this:

 ~{if length(reads) > 0 then sep(" ", reads) else ""}

When running this, cromwell threw the following errors:

Cannot invoke 'sep' on type 'Array[Array[_]]'. Expected an Array[String]

[junyk]

Hi @illusional, just want to double check that this is something we have not implemented yet (or could it be just incorrect Janis syntax in declaring the ToolInput). Thanks!

[illusional]

Hey @junyk, the closest think you can do is .flatten() the input selector and then .join('separator'). In CWL you could implement a JS .map(el => func), and this is a relevant issue for WDL: openwdl/wdl#203

[junyk]

@illusional Good tip. Thanks Michael! : )