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bioforensics / yeat

YEAT: Your Everyday Assembly Tool
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Single-end Support #50

Closed danejo3 closed 10 months ago

danejo3 commented 10 months ago

The purpose of this PR is to resolve #48, integrate single-end read support, fix some bugs introduced in #47, and clean up the test suite.

In issue thread #48, a request was made to increase the filtering process with fastp. By default, fastp will discard reads that are 15 bp or less. Instead of int [=15], we increased the cutoff to [=50]. In addition to the new cutoff range, when paired-end reads are passed into the fastp rule, we call --detect_adapter_for_pe to detect and remove adapters.

Because #48, mentioned not to call --detect_adapter_for_pe for single-end reads, I went ahead and integrated single-end read support with spades, megahit, and Unicycler.

In #47, Oxford Read Support was introduced. In the test suite, I noticed that there were some tests that did not test the new feature. While fixing it, I got slightly frustrated with the test suite and decided to clean it up and remove unnecessary, redundant configuration test files. In this PR, correct Oxford tests were introduced, and test data were consolidated and cleaned up.

danejo3 commented 10 months ago

Okay, I added all the suggested changes to the branch. I think if you pull from this branch the nanofilt problem should be fixed. I ran into this problem as well and somehow fixed it in this branch.