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Fixbug: output of annovar

master
YaqingLiu 4 vuotta sitten
vanhempi
commit
2721c985ab
1 muutettua tiedostoa jossa 3 lisäystä ja 3 poistoa
  1. +3
    -3
      tasks/annovar.wdl

+ 3
- 3
tasks/annovar.wdl Näytä tiedosto

set -o pipefail set -o pipefail
set -e set -e
nt=$(nproc) nt=$(nproc)
/installations/annovar/table_annovar.pl ${vcf} ${database} -buildver hg38 -hgvs -out ${annotated_vcf} -remove -protocol refGene,cytoBand,genomicSuperDups,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad211_exome,clinvar_20200316 -operation g,r,r,f,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
/installations/annovar/table_annovar.pl ${vcf} ${database} -buildver ${hg} -out ${annotated_vcf} -remove -protocol refGene,cytoBand,genomicSuperDups,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad211_exome,clinvar_20200316 -operation g,r,r,f,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
>>> >>>
runtime { runtime {


output { output {
File avinput = "${annotated_vcf}.avinput" File avinput = "${annotated_vcf}.avinput"
File multianno_txt = "${annotated_vcf}.multianno.txt"
File multianno = "${annotated_vcf}.multianno.vcf"
File multianno_txt = "${annotated_vcf}.${hg}_multianno.txt"
File multianno = "${annotated_vcf}.${hg}_multianno.vcf"
} }
} }

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