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seppinho / nft-vcf

nf-test plugin to provide support for VCF files.
MIT License
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Differences in `phasedAutodetect` based on different Nextflow versions #5

Open atrigila opened 1 month ago

atrigila commented 1 month ago

Hi! Thanks for developing this plugin. We are using it in nf-core/phaseimpute. Recently, we found a difference in behavior between different versions of Nextflow and nft-vcf when submitting a PR.

The failure occurs in the following part of the log:

!  99     "VcfFile [chromosomes=[chr21, chr22], sampleCount=1, variantCount=1739, phased=true, phasedAutodetect=false]"

When using Nextflow version 24.04.4, there is a difference where phasedAutodetect is set to false instead of true.

seppinho commented 3 days ago

Interesting. Does this issue still persist? phasedAutodetect only checks if the first line is phased or not, with the default value being true. Do you have a test file I could use to investigate this further?