Rename nextclade2 to nextclade
Issue:
Sister PRs:
@@ -462,8 +462,8 @@ rule prepare_nextclade:
conda: config["conda_environment"]
shell:
"""
- nextclade2 --version
- nextclade2 dataset get --name {params.name} --output-zip {output.nextclade_dataset}
+ nextclade --version
+ nextclade dataset get --name {params.name} --output-zip {output.nextclade_dataset}
"""
rule build_align:
@@ -499,7 +499,7 @@ rule build_align:
--sequences {input.sequences} \
--strip-prefixes {params.strain_prefixes:q} \
--output /dev/stdout 2> {params.sanitize_log} \
- | nextclade2 run \
+ | nextclade run \
--jobs {threads} \
--input-dataset {input.nextclade_dataset} \
--output-tsv {output.nextclade_qc} \
