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:
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]
For some Bioinformatics tool, we may want to pass more than one pair of FASTQ files.
In Janis, it is declared like this:
In wdl, this input was translated into:
The command argument looked like this:
When running this, cromwell threw the following errors: