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ksumngs / yavsap

Yet Another Viral Subspecies Analysis Pipeline
https://ksumngs.github.io/yavsap
MIT License
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[Bug]: No visualizer output for Nanopore reads #41

Closed MillironX closed 2 years ago

MillironX commented 2 years ago

Behavior

Expected behavior

Running yavsap on Nanopore read input should output a file at ${params.outdir}/report/index.html.

Current behavior

The processes PRESENTATION:ECHO2TSV and PRESENTATION:SEQUENCETABLE don't run and The Visualizer isn't output.

Steps to reproduce

Command(s) used to run the pipeline

nextflow run ksumngs/yavsap -profile test_nanopore

Pipeline Output

Log file

nextflow.log

Results folder

yavsap-results.tar.gz

Additional Info

Possible Solution

This appears to be caused by HapLink's lack of producing a unique name for each haplotype prior to v0.6. Could be fixed by upgrading HapLink and reworking the process channels around it.

Environment

MillironX commented 2 years ago

This has been partially fixed by v0.7.1, but we will need to see https://github.com/ksumngs/HapLink.jl/issues/26 resolved before this can be fully fixed.