Merge pull request #226 from nextstrain/nextclade2

Version nextclade binary for transition, i.e. nextclade -> nextclade2
nextstrain · Jan 15, 2024 · 5d3a267 · 5d3a267
2 parents eccb6c3 + 3683aed
commit 5d3a267
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/ingest/workflow/snakemake_rules/nextclade.smk b/ingest/workflow/snakemake_rules/nextclade.smk
@@ -32,7 +32,7 @@ rule align:
     threads: 4
     shell:
         """
-        nextclade run -D {input.dataset} -j {threads}   --retry-reverse-complement \
+        nextclade2 run -D {input.dataset} -j {threads}   --retry-reverse-complement \
                   --output-fasta {output.alignment}  --output-translations {params.translations} \
                   --output-insertions {output.insertions} {input.sequences}
         zip -rj {output.translations} data/translations
@@ -48,7 +48,7 @@ rule nextclade:
     threads: 4
     shell:
         """
-        nextclade run -D {input.dataset} -j {threads} --output-tsv {output}  {input.sequences}  --retry-reverse-complement
+        nextclade2 run -D {input.dataset} -j {threads} --output-tsv {output}  {input.sequences}  --retry-reverse-complement
         """