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

Jump to bottom

set "-o pipefail" for filter_subsample_sequences and mafft_one_chr #173

Merged
merged 1 commit into from
Nov 25, 2020
Merged

set "-o pipefail" for filter_subsample_sequences and mafft_one_chr #173

Changes from all commits
Commits
Show all changes
1 commit
Select commit
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
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 @@ -128,7 +128,7 @@ task filter_subsample_sequences {
}
String out_fname = sub(sub(basename(sequences_fasta), ".vcf", ".filtered.vcf"), ".fasta$", ".filtered.fasta")
command {
set -e
set -e -o pipefail
augur version > VERSION

touch wherefile
Expand Down Expand Up @@ -265,7 +265,7 @@ task mafft_one_chr {
Int cpus = 32
}
command {
set -e
set -e -o pipefail
touch args.txt

# boolean options
Expand Down