Remove url-based uploads and check for missing files

[codecov[bot]]

Codecov Report

Merging #106 (17cb2b8) into master (8c00169) will decrease coverage by 0.13%. The diff coverage is 40.00%.

@@             Coverage Diff              @@
##             master     #106      +/-   ##
============================================
- Coverage     51.47%   51.35%   -0.13%     
+ Complexity      678      676       -2     
============================================
  Files            59       59              
  Lines          4538     4518      -20     
  Branches        570      567       -3     
============================================
- Hits           2336     2320      -16     
+ Misses         2024     2021       -3     
+ Partials        178      177       -1     

Impacted Files	Coverage Δ
...epi/imputationserver/steps/FastQualityControl.java	71.72% <14.28%> (-1.70%)	:arrow_down:
...genepi/imputationserver/steps/InputValidation.java	75.56% <100.00%> (+1.67%)	:arrow_up:

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