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Code polishing for Compress Annotated VCFs #602

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merged 3 commits into from
Jun 20, 2018

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maxulysse
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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
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@szilvajuhos That was meant to be with PR #599

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@szilvajuhos szilvajuhos left a comment

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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.

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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

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

@szilvajuhos szilvajuhos merged commit 3936cca into SciLifeLab:master Jun 20, 2018
@maxulysse maxulysse deleted the CompressAnnVCFs branch June 20, 2018 11:34
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2 participants