Patlas recipes

[tiagofilipe12]

Although this PR started with the addition of pATLAS recipes it ended up:

• Changing the philosophy behind recipes
• Fixing minor issues with args (-l, -L and -o)
• Added new arg -cr, which is used to check the pipeline_string of recipes.

[codecov-io]

Codecov Report

Merging #92 into dev will decrease coverage by 0.12%.
The diff coverage is 57.14%.

@@            Coverage Diff            @@
##              dev     #92      +/-   ##
=========================================
- Coverage   43.62%   43.5%   -0.13%     
=========================================
  Files          49      49              
  Lines        4548    4547       -1     
=========================================
- Hits         1984    1978       -6     
- Misses       2564    2569       +5

Impacted Files	Coverage Δ
flowcraft/tests/test_assemblerflow.py	100% <ø> (ø)	⬆️
flowcraft/tests/test_process_details.py	100% <100%> (ø)	⬆️
flowcraft/generator/process_details.py	100% <100%> (+5.4%)	⬆️
flowcraft/flowcraft.py	64.28% <31.25%> (-4.18%)	⬇️
flowcraft/generator/recipe.py	12.42% <66.66%> (-0.39%)	⬇️

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update a2f24c5...2de23e0. Read the comment docs.