Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

update nextclade and vadr docker images #433

Merged
merged 2 commits into from
Jul 12, 2022
Merged

update nextclade and vadr docker images #433

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
2a2d2c3
bump nextclade 2.0.0 to 2.3.0
dpark01 Jul 12, 2022
523d44c
vadr update
dpark01 Jul 12, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion pipes/WDL/tasks/tasks_ncbi.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -924,7 +924,7 @@ task vadr {
File genome_fasta
String vadr_opts = "--glsearch -s -r --nomisc --mkey sarscov2 --lowsim5seq 6 --lowsim3seq 6 --alt_fail lowscore,insertnn,deletinn"

String docker = "quay.io/staphb/vadr:1.4.1-models-1.3-2"
String docker = "quay.io/staphb/vadr:1.4.2"
Int minlen = 50
Int maxlen = 30000
}
Expand Down
4 changes: 2 additions & 2 deletions pipes/WDL/tasks/tasks_nextstrain.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ task nextclade_one_sample {
File? pcr_primers_csv
File? virus_properties
String? dataset_name
String docker = "nextstrain/nextclade:2.0.0"
String docker = "nextstrain/nextclade:2.3.0"
}
String basename = basename(genome_fasta, ".fasta")
command {
Expand Down Expand Up @@ -98,7 +98,7 @@ task nextclade_many_samples {
String? dataset_name
String basename
File? genome_ids_setdefault_blank
String docker = "nextstrain/nextclade:2.0.0"
String docker = "nextstrain/nextclade:2.3.0"
}
command <<<
set -e
Expand Down
2 changes: 1 addition & 1 deletion requirements-modules.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,4 +8,4 @@ broadinstitute/ncbi-tools=2.10.7.10
nextstrain/base=build-20211012T204409Z
andersenlabapps/ivar=1.3.1
quay.io/staphb/pangolin=4.1.1-pdata-1.11
nextstrain/nextclade=2.0.0
nextstrain/nextclade=2.3.0