From 02657b0874a49ced660c64fd5f034e90e8c829c2 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Fri, 12 Mar 2021 11:35:50 -0500 Subject: [PATCH 1/2] remove the --lowsim3term as per request of Genbank after discussion with Linda and Eric. default is 15 when unspecified. add the new insertnn/deletinn alerts --- pipes/WDL/tasks/tasks_ncbi.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipes/WDL/tasks/tasks_ncbi.wdl b/pipes/WDL/tasks/tasks_ncbi.wdl index 6b4903ac5..0e369cc25 100644 --- a/pipes/WDL/tasks/tasks_ncbi.wdl +++ b/pipes/WDL/tasks/tasks_ncbi.wdl @@ -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 --lowsim5term 2 --fstlowthr 0.0 --alt_fail lowscore,fsthicnf,fstlocnf,insertnn,deletinn" String docker="staphb/vadr:1.1.3" } From 28da41eb78ff3b8e006391df116a004bc480d3ca Mon Sep 17 00:00:00 2001 From: Danny Park Date: Fri, 12 Mar 2021 11:40:11 -0500 Subject: [PATCH 2/2] Linda says drop the lowsim5term too --- pipes/WDL/tasks/tasks_ncbi.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipes/WDL/tasks/tasks_ncbi.wdl b/pipes/WDL/tasks/tasks_ncbi.wdl index 0e369cc25..ff45f0567 100644 --- a/pipes/WDL/tasks/tasks_ncbi.wdl +++ b/pipes/WDL/tasks/tasks_ncbi.wdl @@ -827,7 +827,7 @@ task vadr { } input { File genome_fasta - String vadr_opts="-s -r --nomisc --mkey NC_045512 --lowsim5term 2 --fstlowthr 0.0 --alt_fail lowscore,fsthicnf,fstlocnf,insertnn,deletinn" + 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" }