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

Closed cimendes closed 5 years ago

cimendes commented 5 years ago

Currently, the trimmomatic module fails when the phred encoding is unable to be determined. This can be avoided if the encoding is set to phred33 in these cases. I've tested with a few samples and it works well. It's also what is done in the INNUca pipeline.

codecov-io commented 5 years ago

Codecov Report

Merging #211 into dev will decrease coverage by <.01%. The diff coverage is 25.64%.

Impacted file tree graph

@@            Coverage Diff             @@
##              dev     #211      +/-   ##
==========================================
- Coverage   41.97%   41.96%   -0.01%     
==========================================
  Files          72       72              
  Lines        6464     6486      +22     
==========================================
+ Hits         2713     2722       +9     
- Misses       3751     3764      +13
Impacted Files Coverage Δ
flowcraft/tests/test_flowcraft.py 100% <ø> (ø)
flowcraft/templates/trimmomatic.py 0% <0%> (ø) :arrow_up:
flowcraft/generator/components/metagenomics.py 100% <100%> (ø) :arrow_up:

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cimendes commented 5 years ago

To better mimic innuca's behaviour, if a run fails while the encoding is set to phred33, trimmomatic is retried with the phred64 encoding.