Add select_all miniwdl Stdlib function

[kinow]

No description provided.

[codecov]

Codecov Report

Merging #161 (008dab0) into main (c0e477d) will increase coverage by 0.26%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main     #161      +/-   ##
==========================================
+ Coverage   90.61%   90.88%   +0.26%     
==========================================
  Files           3        3              
  Lines         618      625       +7     
  Branches      180      183       +3     
==========================================
+ Hits          560      568       +8     
  Misses         25       25              
+ Partials       33       32       -1     

Impacted Files	Coverage Δ
wdl2cwl/main.py	90.70% <100.00%> (+0.28%)	⬆️

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[mr-c]

select_all is typically paired with if or scatter in WDL, so it might be a bit soon to implement this.

Can you make your branch on the main repo? It makes it simpler to collaborate :-)

Maybe consider using https://github.com/griffithlab/analysis-wdls/blob/25cf2010055d79bf7df63ab832363066eba87a26/definitions/subworkflows/merge_svs.wdll as an example? There select_all on a source selector for a workflow step could be represented in CWL by using pickValue: all_non_null

[mr-c]

@kinow I ran your CWL code, but it always returns empty arrays for me. I had to make the following adjustment
of adding return before the element comparisons.

        outputEval: $([inputs.one, inputs.two, 1, [inputs.two, inputs.one].find(function(element)
            { return element !== null }) ].filter(function(element) { return element !== null })
            )

[kinow]

For later, happy if anyone (@mr-c ? 😬 ) takes over 👍