update with changes in dev #223

cimendes · 2019-09-16T13:40:51Z

No description provided.

* 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

codecov-io · 2019-09-16T13:40:54Z

Codecov Report

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

@@             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 added 3 commits July 4, 2019 10:59

Dag files (#209)

c8a8574

* 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

Set phred encoding when it fails to be determined - trimmomatic (#211)

658e6db

* fix bug publishdir (downsample_fastq component) * add pphred33 when encoding fails to be determined, if still fails retry with phred64 encoding (trimmomatic component)

Fix downsample (#222)

a2074ca

* edited file names for downsample fastqs * stringified depth for file name

cimendes merged commit 22985ae into fix_219 Sep 16, 2019

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update with changes in dev #223

update with changes in dev #223

cimendes commented Sep 16, 2019

codecov-io commented Sep 16, 2019 •

edited

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update with changes in dev #223

update with changes in dev #223

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cimendes commented Sep 16, 2019

codecov-io commented Sep 16, 2019 • edited Loading

Codecov Report

codecov-io commented Sep 16, 2019 •

edited

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