fix: add extract gisaid env (#235)

* Add pandas.env * Add pandas.env to rule
IKIM-Essen · Sep 8, 2021 · 2b94752 · 2b94752
1 parent 042d0c0
commit 2b94752
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diff --git a/workflow/envs/pandas.yaml b/workflow/envs/pandas.yaml
@@ -0,0 +1,4 @@
+channels:
+  - conda-forge
+dependencies:
+  - pandas =1.3
diff --git a/workflow/rules/strain_calling.smk b/workflow/rules/strain_calling.smk
@@ -9,6 +9,8 @@ checkpoint extract_strain_genomes_from_gisaid:
         save_strains_to=lambda wildcards: config["strain-calling"][
             "extracted-strain-genomes"
         ],
+    conda:
+        "../envs/pandas.yaml"
     script:
         "../scripts/extract-strains-from-gisaid-provision.py"