WDL: specify directory as input.

09 February 2023 00:00
4 comments

(will I'm trying to run nextflow, I'm playing with small WDL workflows)

I've got a workflow that needs a directory as input (I've got a task with `find ~ {dir} -type f (...)` )

It looks like Directory was defined in WDL1.1 https://github.com/openwdl/wdl/blob/main/versions/development/SPEC.md#task-inputs

but it's not parsed in

```

$ java -jar wdlTools-0.17.15.jar check my.wdl

===============================

Type-check errors in my.wdl

===============================

Line:Col | Description

-------------------------------

6:8-6:32 | struct Directory has not been defined

6:8-6:32 | dir value "NO_DIR" of type String is not coercible to Any

37:8-37:21 | struct Directory has not been defined

```

I compiled it with `File` instead of `Directory` , but the web GUI really wants a plain File.

I'm going to try with a String and a full path (but I'm not really sure of what is a full path here, can I use a file ID instead of a path with blank spaces ?)

Or is there any other way to specify an input directory ?

thanks.

Comments

4 comments

Former User of DNAx Community_46
- 09 February 2023 15:06
setting a plain path such as `/Bulk/Whole genome sequences/`, quoted, doesn't work (no such file or directory)

0
Ondrej Klempir DNAnexus Team
- 10 February 2023 13:33
Hi @Pierre LIndenbaum?,

For using " Directory" type,
1. make sure that the WDL script uses version development (I am not sure if it is also in 1.1)
2. Directory type input needs to be in the DNAnexus URI format (e.g. dx://project-xyz:path/to/folder/)
That should be enough for it to compile successfully.
0
Former User of DNAx Community_46
- 14 February 2023 13:31
I got another answer from the support. Here is a snapshot of the answer:

> In order to distinguish between inputs related only to a particular stage and whole workflow, stage-common "prefix" is used for the latter:
>
> https://documentation.dnanexus.com/developer/building-and-executing-portable-containers-for-bioinformatics-software/dxcompiler#compiling-and-running-a-workflow
>
> With that in mind, the content of params.json would then look like:
```
{
"stage-common.bed":"dx://bllablabla",
"stage-common.dir":"dx://bliblabli"
}
```

0
Former User of DNAx Community_46
- 14 February 2023 14:09
also , the answer to the original question was to switch the WDL version to `2.0` .

````
version 2.0

workflow MY_WORKFLOW {

input {
Directory dir
(...)
```

0

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