Fix path pattern for rephased VCF files

[Tim-Yu]

Missing output file(s) phasing_output/*.rephased.vcf.gz expected by process `INTGENOMICSLAB_LRSOMATIC:LRSOMATIC:WAKHAN

The WAKHAN is generating /rephased.vcf.gz and /rephased.vcf.gz.csi
Just incase, I preserved the * for other potential matching
#128

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• This comment contains a description of changes (with reason).

[ljwharbers]

Looks good, feel free to merge after the run nf-test completes. You can ignore the template version fail for now.

PS: We will update wakhan to 0.4.2 next week, so this should resolve some wakhan related issues hopefully as well. If you want, you can include the version bump already here, but we have then not yet tested this.

[ljwharbers]

To update wakhan:

    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/wakhan:0.4.2--pyhdfd78af_0':
        'biocontainers/wakhan:0.4.2--pyhdfd78af_0' }"

[ljwharbers]

Also update the environment.yml file to 0.4.2.