wdl 1.1 `sep()` vs command block `~{sep}` return different values

[Ben-Habermeyer]

Hi DXCompiler team, I recently came across a behavior when trying to convert an array of File into a CLI arg

I have an input Array[File] snp_vcfs

Originally in a command block I had given this to a CLI tool like the following --sample-snp-vcfs ~{sep=' ' snp_vcfs}

Which resulted in the following resolution when run on DNAnexus --sample-snp-vcfs /home/dnanexus/inputs/input4994899743764944893/s_1_AACATACTGAGTGATCCGGA.final.vcf /home/dnanexus/inputs/input4994899743764944893/s_1_AATCACGGTTCGGATCGGTT.final.vcf

But then I needed to make this optional, so I put the following in my task block for the input Array[File] snp_vcfs = []

And added this arg String snp_vcfs_args = if length(snp_vcfs) > 0 then "--sample-snp-vcfs " + sep(" ", snp_vcfs) else ""

Which I reference in command block ~{snp_vcfs_args} but this looks resolves as the following --sample-snp-vcfs dx://file-GQZPx0Q0xKpKqJp3kxZ4XBP8::/s_1_AACATACTGAGTGATCCGGA.final.vcf dx://file-GQZKf9Q0GxY4K65ZPqGYkp4Y::/s_1_AATCACGGTTCGGATCGGTT.final.vcf

Is it possible for the 1.1 builtin sep() to resolve File objects to their path (like the ~{sep} does) i.e. /home/dnanexus/inputs/... rather than just converting them to strings (and rendering these paths potentially unusable)?

1.1 says ~{sep} is deprecated but I feel like they should have the same behavior unless there is something I'm missing? Thanks

[Gvaihir]

This might be the implementation thing in dxC. I'll track internally, thanks for reporting

[Gvaihir]

@Ben-Habermeyer - I started working on this issue. Could you clarify:

1. But then I needed to make this optional, so I put the following in my task block for the input Array[File] snp_vcfs = [] <- This does not look like an optional declaration. It's a defined array which is supposedly evaluated to an empty string in your conditional, if empty. Please clarify - is this what you mean? This is essential for the next point
2. The difference between the Placeholder Options ~{sep=' ' snp_vcfs} (let's call it "case A") and sep() ("case B") - is that case A localized the files to the workers, but case B did not. Going back to point 1 - did you declare snp_vcfs as optional or not? I mean Array[File]? or Array[File?]. If they were optionals for Case B and not for case A and you chose to stream files - they may not be localized in the correct time or manner. Anyway - please provide a minimal wdl source and a compile flags you used.