Not all definitions in JSON schema have a "properties", leading to an error

[drpatelh]

Closes #1419

[codecov]

Codecov Report

Merging #1521 (a494d27) into dev (1685277) will decrease coverage by 0.01%.
The diff coverage is 57.14%.

@@            Coverage Diff             @@
##              dev    #1521      +/-   ##
==========================================
- Coverage   64.61%   64.59%   -0.02%     
==========================================
  Files          54       54              
  Lines        6178     6192      +14     
==========================================
+ Hits         3992     4000       +8     
- Misses       2186     2192       +6     

Impacted Files	Coverage Δ
nf_core/schema.py	77.24% <57.14%> (-0.61%)	⬇️

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[ewels]

Working on this PR at the moment so no need to change, but FYI we are trying to slowly move everything to the new format string style in the codebase now (with a few exceptions where this old style is still clearer). Generally it's much easier to read and maintain.

So here it'd be:

Suggested change

	allOf = {"$ref": "#/definitions/{}".format(d_key)}
	allOf = {"$ref": f"#/definitions/{d_key}"}

Just prepend the string quotes with f and then stick the variable name into the squiggly brackets.

[ewels]

I rewrote this whole function to use Python list comprehension so that you didn't need to use deep copies. But the code ended up being uglier so I ditched it. Then I realised that you didn't actually need deep copies with your existing code 😅

Minor cleanup, hope that's ok. LGTM now 👍🏻

Changes:

• Added log warning
• Use get to avoid crashes if properties or allOf keys not set
• Moved function call out of function to remove missing config parameters
• Added call to the function on the object returned from the web builder