Code polishing for Compress Annotated VCFs

[maxulysse]

Simplification of channels.

Output is now:

• _snpEff.ann.vcf.gz instead of .snpEff.ann.vcf.gz
• _VEP.ann.vcf.gz instead of .vep.ann.vcf.gz
• _snpEff_VEP.ann.vcf.gz instead of .snpEff.ann.vcf.vep.ann.vcf.gz

[maxulysse]

@szilvajuhos That was meant to be with PR #599

[szilvajuhos]

Do we really have to change basename to simplename? basename has a meaning/command in UNIX, simplename is something new we can not realte to.

[maxulysse]

baseName from sample.vcf.gz will get sample.vcf
So then we're getting .snpEff.ann.vcf.vep.ann.vcf.gz which is quite a long name.
simpleName get only what is before the first .
So with simpleName it will reduce that to only _snpEff_VEP.ann.vcf.gz

[maxulysse]

And in this case baseName, simpleName or fileName are all used within Nextflow, so it's groovy magic in fact ;-)