Running SnpEff and VEP at once, also fixing CLI for annotators #555
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annotate.nf
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| def defineStepList() { | ||
| return [ | ||
| 'annotate' |
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We don't need this defineStepList function anymore.
Only one step is available at this point.
annotate.nf
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| 'bcftoolsStats' : 'Reports/BCFToolsStats', | ||
| 'snpeff' : 'Annotation/SnpEff', | ||
| 'vep' : 'Annotation/VEP', | ||
| 'merge' : 'Annotation/merged' |
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I believe that there is a merging error here.
The definition of the directory map happens once here, and once in the defineStepList.
| @@ -222,7 +241,8 @@ def defineDirectoryMap() { | |||
| def defineToolList() { | |||
| return [ | |||
| 'snpeff', | |||
| 'vep' | |||
| 'vep', | |||
| 'merge' | |||
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I prefer lists to be sorted, but that's not really important here ;-)
| @@ -1165,3 +1160,307 @@ chrY 1187549 1212750 CRLF2 | |||
| chrY 1268800 1310381 CSF2RA | |||
| chrY 1462572 1537107 P2RY8 | |||
| chrY 2691179 2741309 CD99 | |||
| chr1 1785285 1891117 GNB1 | |||
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Why do we have so many changes in this file?
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Long story short: it is a quasi-panel, ever-expanding list of genes related to cancers.
| // we have to exchange the channels | ||
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| if('merge' in tools) { | ||
| vcfForVep = snpEffOutputVCFs |
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So if I want to have snpEFF, VEP and merged VCF it's not possible?
Can't we use that?
vcfForVep = vcfForVep.mix(snpEffOutputVCFs)
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That will be a new feature if it is going to be needed at all. Testing takes time and I do not want to add stuff that is never going to be used or relatively easy to do with some scripting.
maxulysse
changed the title
Running SnpEff an VEP at once, also fixing CLI for annotators
Resolving #547