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assemblerflow / flowcraft

FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. :whale::package:
GNU General Public License v3.0
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Dag files #209

Closed cimendes closed 5 years ago

cimendes commented 5 years ago

This PR addresses an issue raised in #194 where the .treeDag.json and forktree.json files aren't automatically staged when publishing the resulting FlowCraft pipelines to a repository. As they are hidden files, they are often overlooked, breaking the execution of the pipelines when run remotely.

There was no reason to keep these files as dotfiles, so they were moved to the resources folder.

codecov-io commented 5 years ago

Codecov Report

Merging #209 into dev will increase coverage by 0.01%. The diff coverage is 66.66%.

Impacted file tree graph

@@            Coverage Diff             @@
##              dev     #209      +/-   ##
==========================================
+ Coverage   41.95%   41.97%   +0.01%     
==========================================
  Files          72       72              
  Lines        6461     6464       +3     
==========================================
+ Hits         2711     2713       +2     
- Misses       3750     3751       +1
Impacted Files Coverage Δ
flowcraft/generator/error_handling.py 85% <ø> (ø) :arrow_up:
flowcraft/generator/components/variant_calling.py 100% <ø> (ø) :arrow_up:
flowcraft/generator/components/mapping.py 100% <ø> (ø) :arrow_up:
flowcraft/generator/inspect.py 10.47% <0%> (ø) :arrow_up:
flowcraft/templates/downsample_fastq.py 0% <0%> (ø) :arrow_up:
flowcraft/generator/engine.py 87.88% <100%> (+0.02%) :arrow_up:
flowcraft/flowcraft.py 60.62% <100%> (ø) :arrow_up:
flowcraft/tests/test_assemblerflow.py 100% <100%> (ø) :arrow_up:

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cimendes commented 5 years ago

The verification was moved to the render_pipeline function and the function to write the json was made more general to accommodate both forktree.json and treedag.json files. Thanks @ODiogoSilva for pointing out my very silly mistake!