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Uses the MiniWDL parser and maps back to Janis. Only works for simple task definitions, workflow support still to come.
Still a few issues with a WDL string potentially still having placeholders in it, but it's a good starting point.

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Test Failed for group 602eff8946ca000904222e6b.

SamTools:

  • SamToolsFlagstat.basic (dev - cromwell): Test Succeeded
  • SamToolsFlagstat.basic (Spartan - cromwell): Test Succeeded

WGSGermlineGATK:

  • WGSGermlineGATK.brca1 (Spartan - cromwell): Test Failed 602eff8946ca000904222e6e

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codecov-io commented Mar 11, 2021

Codecov Report

Merging #68 (85e1960) into master (bcbc1da) will decrease coverage by 4.83%.
The diff coverage is 7.35%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master      #68      +/-   ##
==========================================
- Coverage   69.12%   64.28%   -4.84%     
==========================================
  Files          78       80       +2     
  Lines       10282    11139     +857     
==========================================
+ Hits         7107     7161      +54     
- Misses       3175     3978     +803     
Impacted Files Coverage Δ
janis_core/ingestion/fromwdl.py 0.00% <0.00%> (ø)
janis_core/translations/hailbatch.py 0.00% <0.00%> (ø)
janis_core/translations/janis.py 0.00% <0.00%> (ø)
janis_core/operators/stringformatter.py 83.82% <16.66%> (-3.10%) ⬇️
janis_core/operators/logical.py 65.65% <34.78%> (-1.39%) ⬇️
janis_core/operators/selectors.py 69.12% <35.29%> (-1.80%) ⬇️
janis_core/operators/standard.py 55.69% <45.07%> (-3.14%) ⬇️
janis_core/operators/operator.py 65.34% <53.33%> (-0.82%) ⬇️
janis_core/workflow/workflow.py 48.01% <66.66%> (+0.08%) ⬆️
janis_core/tests/test_operators.py 98.80% <100.00%> (ø)
... and 3 more

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@illusional
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Closed in favour of: #69

@illusional illusional closed this Mar 16, 2021
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5 participants