diff --git a/ingest/workflow/snakemake_rules/sort.smk b/ingest/workflow/snakemake_rules/sort.smk index cec99cc..d5d6d4f 100644 --- a/ingest/workflow/snakemake_rules/sort.smk +++ b/ingest/workflow/snakemake_rules/sort.smk @@ -20,8 +20,8 @@ rule sort: ''' seqkit rmdup {input.sequences} | \ nextclade3 sort - --output-dir tmp - mv tmp/nextstrain/rsv/b/sequences.fasta > data/b/sequences.fasta - mv tmp/nextstrain/rsv/a/sequences.fasta > data/a/sequences.fasta + mv tmp/nextstrain/rsv/b/sequences.fasta data/b/sequences.fasta + mv tmp/nextstrain/rsv/a/sequences.fasta data/a/sequences.fasta rm -r tmp '''