jsmedmar commented 6 years ago

Hide container options by default and add --help-container to display them.

[x] 🚀 New feature
[x] 🔧 Code refactor
[x] 📘 I have updated the documentation accordingly
[x] ✅ I have added tests to cover my changes

See example:

usage: toil_disambiguate [-h] [-v] [--help-toil] [--help-container]
                         --input_data INPUT_DATA [INPUT_DATA ...]
                         --sample_name SAMPLE_NAME --reference_a REFERENCE_A
                         --reference_b REFERENCE_B
                         [--max_cores_usage MAX_CORES_USAGE]
                         [--max_memory_usage MAX_MEMORY_USAGE]
                         [--keep_intermediates]
                         jobStore

toil_disambiguate pipeline

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  --help-toil           show help with toil arguments and exit
  --help-container      show help with container arguments and exit

pipeline arguments:
  --outdir OUTDIR       path to output directory (default: None)
  ...

toil arguments:
  jobStore              the location of the job store for the workflow. See
                        --help-toil for more toil options and information
                        [REQUIRED]

codecov[bot] commented 6 years ago

Codecov Report

Merging #18 into master will increase coverage by 0.82%. The diff coverage is 100%.

@@           Coverage Diff            @@
##           master    #18      +/-   ##
========================================
+ Coverage   99.17%   100%   +0.82%     
========================================
  Files           5      5              
  Lines         243    256      +13     
========================================
+ Hits          241    256      +15     
+ Misses          2      0       -2

Impacted Files	Coverage Δ
toil_container/containers.py	`100% <100%> (+1.94%)`	:arrow_up:
toil_container/parsers.py	`100% <100%> (ø)`	:arrow_up:

Continue to review full report at Codecov.

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jsmedmar commented 6 years ago

@juanesarango, this is ready for review + merge :shipit:

papaemmelab / toil_container

🚀 add help container feature #18

Codecov Report