How to provide a Struct as an input to a WDL workflow.

I'm trying to provide an Array of these structs:

```

struct VcfChunk {

String chrom

String start_pos

String end_pos

File vcf

File csi

}

```

to a workflow via json and am receiving this cryptic error:

keys (TreeSet(chrom, csi, pos_end, pos_start, vcf)) have members that do not appear in struct VcfChunk

The input json is here and the full workflow script here.

I would also be fine using read_tsv but it looks like that won't generate correct dnanexus_link for the Files?

thanks,

Jared

3 comments

Chai Fungtammasan DNAnexus Team
- 04 November 2022 20:25
Yes, our dxCompiler and platform support Struct.
In this case, it's the error in name of your argument. When you defined it, you use `start_pos`, but when you call it you say `pos_start`. Same for ending position.

0
Former User of DNAx Community_18
- 04 November 2022 20:58
Well that is embarrassing! I can confirm it is working now.

Thanks again,

Jared

0
Chai Fungtammasan DNAnexus Team
- 04 November 2022 23:15
No worries. The community got your back. :)

0

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