Differences in phasedAutodetect based on different Nextflow versions

[atrigila]

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.

• Nextflow Version: latest-everything (24.07.0-edge)
  Successful Run Log

• Nextflow Version: 24.04.4
  Failed Run Log

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]

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?