wdl
wdl copied to clipboard
openwdl
Workflow Description Language - Specification and Implementations
I would like to be able to create type aliases, namely something like this: ``` ... type PathToFastq = File type PathToFasta = File ... task bwa { input {...
Cross-posted from #405 Also see discussions here: * https://github.com/openwdl/wdl/discussions/413 * https://github.com/openwdl/wdl/discussions/407 Currently, the WDL specification provides a small library of functions that meet the needs of many use-cases, but certainly...
In V1, File + String = File is allowed. In development, String + File = File is allowed, but File + String is removed. I am guessing this was a...
I'm sitting down to try to summarize the convo about getting data read into an array of Structs. The situation arose from the removal of the `read_objects` function, which could...
I would like to be able to read TSV with headers, where each raw will become Map. So, I will be able to say raw["myheader"] instead of memorizing which number...
I have a `Map[String,File]` from which I want to extract the values into an `Array[File]`, that would be equivalent to eg the Java expression `List list = map.values`. **Justification:** I...
Currently, the spec says: "When a WDL author uses a File input in their **Command Section**, the fully qualified, localized path to the file is substituted into the command string."...
# Automatic coercions considered harmful Authors: O. Rodeh with J. Didion (DNAnexus Inc.) This issue describes a line of thought regarding type checking for WDL programs. It is based on...
else?
I noticed 1) works but not 2). Can we have else for conditional blocks (not just one-liners)? ### 1) ``` workflow merge { Array[File] smallfiles = [] if(length(smallfiles)>2) { call...
As mentioned a couple of times, the pair dereferencing is not intuitive (you have to look it up in the docs to be able to find it). Perhaps we could...
