fix wildcards
@@ -469,7 +469,7 @@ rule prepare_nextclade:
rule build_align:
message:
"""
- Running nextclade QC and aligning sequences to {input.reference}
+ Running nextclade QC and aligning sequences
- gaps relative to reference are considered real
"""
input:
@@ -484,7 +484,7 @@ rule build_align:
outdir = "results/{build_name}/translations",
strain_prefixes=config["strip_strain_prefixes"],
sanitize_log="logs/sanitize_sequences_before_nextclade_{build_name}.txt",
- output_translations = "results/{build_name}/translations/aligned.gene.{{gene}}.fasta"
+ output_translations = "results/{build_name}/translations/aligned.gene.\{gene\}.fasta"
log:
"logs/align_{build_name}.txt"
benchmark:
