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Running SnpEff and VEP at once, also fixing CLI for annotators #555

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Apr 4, 2018
Merged

Running SnpEff and VEP at once, also fixing CLI for annotators #555

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ad3587e
skeleton for merging snpEff and VEP
Mar 12, 2018
d149ba1
hoping removing these will fix the permission error
Mar 13, 2018
1ce19c7
removing UPPMAX dirs
Mar 18, 2018
df2474d
test Singularity containers description
Mar 18, 2018
1c9dfdc
Merge branch 'master' of github.com:szilvajuhos/CAW
Mar 18, 2018
8a9acec
tpypo
Mar 18, 2018
12100cf
VEP and snpEff CLI changes
Mar 27, 2018
91fa5b1
space adjust
Mar 27, 2018
9aee345
additional genes
Mar 27, 2018
bd76442
Merge fixes
Mar 27, 2018
dfd1898
Merge conflict resolved
Apr 3, 2018
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32 changes: 21 additions & 11 deletions annotate.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -141,20 +141,21 @@ process RunSnpeff {

output:
set file("${vcf.baseName}.snpEff.ann.vcf"), file("${vcf.baseName}.snpEff.genes.txt"), file("${vcf.baseName}.snpEff.csv"), file("${vcf.baseName}.snpEff.summary.html") into snpeffReport
set variantCaller,file("${vcf.baseName}.snpEff.ann.vcf") into snpEffOutputVCFs

when: 'snpeff' in tools
when: 'snpeff' in tools || 'merge' in tools

script:
"""
java -Xmx${task.memory.toGiga()}g \
-jar \$SNPEFF_HOME/snpEff.jar \
${snpeffDb} \
-csvStats ${vcf.baseName}.snpEff.csv \
-nodownload \
-cancer \
-v \
${vcf} \
> ${vcf.baseName}.snpEff.ann.vcf
-jar \$SNPEFF_HOME/snpEff.jar \
${snpeffDb} \
-csvStats ${vcf.baseName}.snpEff.csv \
-nodownload \
-canon \
-v \
${vcf} \
> ${vcf.baseName}.snpEff.ann.vcf

mv snpEff_summary.html ${vcf.baseName}.snpEff.summary.html
"""
Expand All @@ -165,6 +166,13 @@ if (params.verbose) snpeffReport = snpeffReport.view {
File : ${it.fileName}"
}

// When we are running in the 'merge' mode (first snpEff, then VEP)
// we have to exchange the channels

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.

}

process RunVEP {
tag {vcf}

Expand All @@ -176,7 +184,7 @@ process RunVEP {
output:
set file("${vcf.baseName}.vep.ann.vcf"), file("${vcf.baseName}.vep.summary.html") into vepReport

when: 'vep' in tools
when: 'vep' in tools || 'merge' in tools

script:
genome = params.genome == 'smallGRCh37' ? 'GRCh37' : params.genome
Expand Down Expand Up @@ -230,7 +238,8 @@ 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 ;-)

]
}

Expand All @@ -252,6 +261,7 @@ def helpMessage() {
log.info " Possible values are:"
log.info " snpeff (use snpEff for Annotation of Variants)"
log.info " vep (use VEP for Annotation of Variants)"
log.info " merge (first snpEff, then feed its output VCFs to VEP)"
log.info " --annotateTools"
log.info " Option to configure which tools to annotate."
log.info " Different tools to be separated by commas."
Expand Down
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