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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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Fix for #219 - Bad python2 file lost in the bin folder #224

Open cimendes opened 5 years ago

cimendes commented 5 years ago

This PR fixes the issues raised in #219. I've moved the problematic file from the bin folder and into templates, updating it to python3. I've also adjusted the components "remove_host" and "retrieve_mapped" to handle this template file.

This change is Reviewable

codecov-io commented 5 years ago

Codecov Report

Merging #224 into dev will decrease coverage by 1%. The diff coverage is 0%.

Impacted file tree graph

@@            Coverage Diff             @@
##              dev     #224      +/-   ##
==========================================
- Coverage   42.34%   41.34%   -1.01%     
==========================================
  Files          72       73       +1     
  Lines        6529     6584      +55     
==========================================
- Hits         2765     2722      -43     
- Misses       3764     3862      +98
Impacted Files Coverage Δ
flowcraft/generator/components/metagenomics.py 100% <ø> (ø) :arrow_up:
flowcraft/generator/components/mapping.py 100% <ø> (ø) :arrow_up:
flowcraft/templates/renamePE_samtoolsFASTQ.py 0% <0%> (ø)

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