From 30b1d5a4860c1822b16f8d55b3e9e577455138e5 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Wed, 8 May 2024 15:57:26 -0700 Subject: [PATCH] fixup: forgot the example files connection --- phylogenetic/rules/prepare_sequences.smk | 4 ++-- phylogenetic/rules/prepare_sequences_E.smk | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/phylogenetic/rules/prepare_sequences.smk b/phylogenetic/rules/prepare_sequences.smk index 203ea9f0..6a0c2675 100644 --- a/phylogenetic/rules/prepare_sequences.smk +++ b/phylogenetic/rules/prepare_sequences.smk @@ -35,7 +35,7 @@ rule decompress: sequences = "data/sequences_{serotype}.fasta.zst", metadata = "data/metadata_{serotype}.tsv.zst" output: - sequences = "data/genome/sequences_{serotype}.fasta", + sequences = "data/sequences_{serotype}.fasta", metadata = "data/metadata_{serotype}.tsv" shell: """ @@ -52,7 +52,7 @@ rule filter: - excluding strains with missing region, country or date metadata """ input: - sequences = "data/{gene}/sequences_{serotype}.fasta", + sequences = "data/sequences_{serotype}.fasta", metadata = "data/metadata_{serotype}.tsv", exclude = config["filter"]["exclude"], output: diff --git a/phylogenetic/rules/prepare_sequences_E.smk b/phylogenetic/rules/prepare_sequences_E.smk index 764c6c11..bf4f0b65 100644 --- a/phylogenetic/rules/prepare_sequences_E.smk +++ b/phylogenetic/rules/prepare_sequences_E.smk @@ -41,7 +41,7 @@ rule align_and_extract_E: Cutting sequences to the length of the E gene reference sequence """ input: - sequences = "data/genome/sequences_{serotype}.fasta", + sequences = "data/sequences_{serotype}.fasta", reference = "results/config/reference_{serotype}_E.fasta" output: sequences = "results/E/sequences_{serotype}.fasta"