add publishDir to link raw joint-call VCFs to the result folder

[bguo068]

https://github.com/bguo068/snp_call_nf/blob/9bbd5284f46a49bb12640892b84ab92d0cb77f98/main.nf#L303C1-L323C2

Currently raw joint-call VCFs are not linked to the result folder. But you can use nextflow log command to show their locations within the work directory if you have run the pipeline successfully in your last call. For example,

nextflow log `nextflow log -q | tail -1` -f workdir  -filter 'name =~ /GATK_GENOTYPE_GVCFS.*/' \
| while read workdir; do ls -d $workdir/*.vcf; done

The workaround might be helpful to you. @Matthew-A-epi