diff --git a/SARS2seq/workflow/envs/Typing.yaml b/SARS2seq/workflow/envs/Typing.yaml index 4d671c7..561a330 100644 --- a/SARS2seq/workflow/envs/Typing.yaml +++ b/SARS2seq/workflow/envs/Typing.yaml @@ -8,7 +8,7 @@ channels: dependencies: - python=3.7 - libffi==3.3 - - pangolin=3.1 + - pangolin==4.0.2 - nextclade=1.10 - snakemake<=6.8.0 - pandas==1.3.5 diff --git a/SARS2seq/workflow/workflow.smk b/SARS2seq/workflow/workflow.smk index ca748ef..61b2355 100644 --- a/SARS2seq/workflow/workflow.smk +++ b/SARS2seq/workflow/workflow.smk @@ -971,8 +971,7 @@ rule update_typingtools: shadow: "minimal" shell: """ - pangolin --update - pangolin --update + pangolin --update-data nextclade dataset get --name='sars-cov-2' --output-dir='{output.nxc_dataset}' """