Set phred encoding when it fails to be determined - trimmomatic #211
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# Conflicts: # flowcraft/tests/test_flowcraft.py
# Conflicts: # changelog.md
cimendes
requested review from
jacarrico,
ODiogoSilva,
bfrgoncalves and
tiagofilipe12
Codecov Report
@@ Coverage Diff @@
## dev #211 +/- ##
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- Coverage 41.97% 41.96% -0.01%
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Files 72 72
Lines 6464 6486 +22
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+ Hits 2713 2722 +9
- Misses 3751 3764 +13
Continue to review full report at Codecov.
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To better mimic innuca's behaviour, if a run fails while the encoding is set to phred33, trimmomatic is retried with the phred64 encoding. |
cimendes
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Sep 16, 2019
* Dag files (#209) * 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) * 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) * edited file names for downsample fastqs * stringified depth for file name
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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.