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vadr option updates #234

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vadr option updates #234

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02657b0
remove the --lowsim3term as per request of Genbank after discussion w…
dpark01 Mar 12, 2021
28da41e
Linda says drop the lowsim5term too
dpark01 Mar 12, 2021
e864fcf
Merge pull request #234 from broadinstitute/dp-genbank
dpark01 Mar 12, 2021
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2 changes: 1 addition & 1 deletion pipes/WDL/tasks/tasks_ncbi.wdl
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Expand Up @@ -827,7 +827,7 @@ task vadr {
}
input {
File genome_fasta
String vadr_opts="-s -r --nomisc --mkey NC_045512 --lowsim5term 2 --lowsim3term 2 --fstlowthr 0.0 --alt_fail lowscore,fsthicnf,fstlocnf"
String vadr_opts="-s -r --nomisc --mkey NC_045512 --fstlowthr 0.0 --alt_fail lowscore,fsthicnf,fstlocnf,insertnn,deletinn"

String docker="staphb/vadr:1.1.3"
}
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