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

fix: Check opensll problems #685

Open
wants to merge 4 commits into
base: master
Choose a base branch
from
Open

fix: Check opensll problems #685

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
08b80c0
Update entrez.yaml
vBassewitz Dec 18, 2024
b977c77
Update ref.smk (just for testing purpose)
vBassewitz Dec 18, 2024
663e567
Update main.yml
vBassewitz Dec 18, 2024
994ec98
Update ref.smk
vBassewitz Dec 18, 2024
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 .github/workflows/main.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -190,7 +190,7 @@ jobs:
run: sudo df -h

Benchmarks-Tests:
runs-on: ubuntu-latest
runs-on: ubuntu-24.04
env:
GISAID_API_TOKEN: ${{ secrets.GISAID_API_TOKEN }}
needs:
Expand Down
1 change: 1 addition & 0 deletions workflow/envs/entrez.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,3 +4,4 @@ channels:
- nodefaults
dependencies:
- entrez-direct =16.2
- openssl =3.4.0
2 changes: 1 addition & 1 deletion workflow/rules/ref.smk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ rule get_genome:
resources:
ncbi_api_requests=1,
shell:
"((esearch -db nucleotide -query '{params.accession}' | "
"openssl version && ((esearch -db nucleotide -query '{params.accession}' | "
"efetch -format fasta > {output}) && [ -s {output} ]) 2> {log}"


Expand Down
Loading