LTR Retriever crashes when input assembly does not contain LTRs - Githubissues

Plant-Food-Research-Open / assemblyqc

A Nextflow pipeline for evaluating assembly quality

https://plant-food-research-open.github.io/assemblyqc/

MIT License

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LTR Retriever crashes when input assembly does not contain LTRs #92

Closed GallVp closed 1 month ago

GallVp commented 1 month ago

Description of the bug

LTR Retriever crashes when input assembly does not contain LTRs

Command used and terminal output

No response

Relevant files

No response

System information

No response

GallVp commented 1 month ago

Tasks to gracefully handle assemblies for which no LTRs are found:

[x] Add unit tests to FASTA_LTRRETRIEVER_LAI relevant modules to verify that they can exit gracefully
[x] Add a pipeline level test to verify that FASTA_LTRRETRIEVER_LAI passes an appropriate log to the reporting module which is then displayed in the report.html

See patch PR: https://github.com/Plant-Food-Research-Open/assemblyqc/pull/106