Fix: Attachments Illumina file pairing - Githubissues

phac-nml / irida-next

IRIDA Next

https://phac-nml.github.io/irida-next/

Apache License 2.0

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Fix: Attachments Illumina file pairing #550

Closed ericenns closed 5 months ago

ericenns commented 5 months ago

What does this PR do and why?

Describe in detail what your merge request does and why.

When running bcl2fastq or bcl2fastq2 with --no-lane-splitting outputted fastq files do not include _LXXX so we need to support illumina files without the lane numbering. This PR adds in support for those files.

Screenshots or screen recordings

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How to set up and validate locally

Numbered steps to set up and validate the change are strongly suggested.

Upload test/fixtures/TestSample_S1_R1_001.fastq and test/fixtures/TestSample_S1_R2_001.fastq to a sample
Verify that the files are paired together and are labelled as illumina_pe for type

PR acceptance checklist

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[x] I have evaluated the PR acceptance checklist for this PR.

github-actions[bot] commented 5 months ago

Simplecov Report

Covered	Threshold
91.88%	90%