change nextclade binary name to include version suffix
@@ -92,12 +92,11 @@ rule align:
--sequences {input.sequences} \
--strip-prefixes {params.strain_prefixes:q} \
--output /dev/stdout 2> {params.sanitize_log} \
- | nextalign run \
+ | nextalign2 run \
--jobs={threads} \
--reference {input.reference} \
--genemap {input.genemap} \
--output-translations {params.output_translations} \
- --output-basename {params.basename} \
--output-fasta {params.uncompressed_alignment} \
--output-insertions {output.insertions} > {log} 2>&1;
xz -2 -T {threads} {params.uncompressed_alignment};
@@ -463,8 +462,8 @@ rule prepare_nextclade:
conda: config["conda_environment"]
shell:
"""
- nextclade --version
- nextclade dataset get --name {params.name} --output-zip {output.nextclade_dataset}
+ nextclade2 --version
+ nextclade2 dataset get --name {params.name} --output-zip {output.nextclade_dataset}
"""
rule build_align:
@@ -500,7 +499,7 @@ rule build_align:
--sequences {input.sequences} \
--strip-prefixes {params.strain_prefixes:q} \
--output /dev/stdout 2> {params.sanitize_log} \
- | nextclade run \
+ | nextclade2 run \
--jobs {threads} \
--input-dataset {input.nextclade_dataset} \
--output-tsv {output.nextclade_qc} \
