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update with changes in dev#223

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cimendes merged 3 commits intofix_219from
dev
Sep 16, 2019
Merged

update with changes in dev#223
cimendes merged 3 commits intofix_219from
dev

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cimendes added 3 commits July 4, 2019 10:59
* move DAG JSON files to the resources directory

* added manifest information to the `nextflow.config` file to allow for remote execution (#204) - Partial solve to #194 issue
- Deprecation of the `manifest.config´ file
* fix bug publishdir (downsample_fastq component)

* add pphred33 when encoding fails to be determined, if still fails retry with phred64 encoding (trimmomatic component)
* edited file names for downsample fastqs
* stringified depth for file name
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codecov-io commented Sep 16, 2019

Codecov Report

Merging #223 into fix_219 will increase coverage by 0.39%.
The diff coverage is 44.77%.

Impacted file tree graph

@@             Coverage Diff             @@
##           fix_219     #223      +/-   ##
===========================================
+ Coverage    41.95%   42.34%   +0.39%     
===========================================
  Files           72       72              
  Lines         6461     6529      +68     
===========================================
+ Hits          2711     2765      +54     
- Misses        3750     3764      +14
Impacted Files Coverage Δ
flowcraft/generator/error_handling.py 85% <ø> (ø) ⬆️
flowcraft/generator/components/variant_calling.py 100% <ø> (ø) ⬆️
flowcraft/generator/components/mapping.py 100% <ø> (ø) ⬆️
flowcraft/templates/trimmomatic.py 0% <0%> (ø) ⬆️
flowcraft/generator/inspect.py 10.47% <0%> (ø) ⬆️
flowcraft/templates/downsample_fastq.py 0% <0%> (ø) ⬆️
flowcraft/generator/engine.py 87.88% <100%> (+0.02%) ⬆️
flowcraft/flowcraft.py 60.62% <100%> (ø) ⬆️
flowcraft/generator/components/metagenomics.py 100% <100%> (ø) ⬆️
flowcraft/tests/test_flowcraft.py 100% <100%> (ø)
... and 2 more

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@cimendes cimendes merged commit 22985ae into fix_219 Sep 16, 2019
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2 participants