Merge pull request #46 from RIVM-bioinformatics/dev

fixate pangolin version
RIVM-bioinformatics · Apr 8, 2022 · 3554b60 · 3554b60
2 parents eb1ac2b + 27e30d3
commit 3554b60
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diff --git 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
@@ -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}'
         """