AWS cores

nextstrain · Apr 30, 2024 · 3e0d85c · 3e0d85c
1 parent 1c421ec
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diff --git a/phylogenetic/README.md b/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/

diff --git a/phylogenetic/rules/prepare_sequences_E.smk b/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} \