AWS cores

phylogenetic/README.md

@@ -62,7 +62,7 @@ example sequences into the `data/` directory like so:
 
 With access to AWS, this can be more quickly run as:
 
-    nextstrain build --aws-batch --aws-batch-cpus 4 --aws-batch-memory 7200 . --jobs 4
+    nextstrain build --aws-batch --aws-batch-cpus 10 --aws-batch-memory 7200 . --jobs 10
 
 [Nextstrain]: https://nextstrain.org
 [augur]: https://docs.nextstrain.org/projects/augur/en/stable/

phylogenetic/rules/prepare_sequences_E.smk

@@ -50,7 +50,7 @@ rule align_and_extract_E:
         min_length = config['filter']['E_min_length'],
     shell:
         """
-        nextclade3 run \
+        nextclade run \
            -j 2 \
            --input-ref {input.reference} \
            --output-fasta {output.sequences} \