Define input paths with literal path strings

https://docs.nextstrain.org/en/latest/reference/snakemake-style-guide.html#define-input-paths-with-literal-path-strings
nextstrain · Jan 11, 2024 · 6349fd7 · 6349fd7
1 parent efe11e3
commit 6349fd7
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Showing 4 changed files with 6 additions and 17 deletions.
diff --git a/phylogenetic/Snakefile b/phylogenetic/Snakefile
@@ -4,17 +4,6 @@ rule all:
     input:
         auspice_json = "auspice/zika.json",
 
-rule files:
-    params:
-        input_fasta = "data/zika.fasta",
-        dropped_strains = "config/dropped_strains.txt",
-        reference = "config/zika_reference.gb",
-        colors = "config/colors.tsv",
-        auspice_config = "config/auspice_config.json",
-        description = "config/description.md"
-
-files = rules.files.params
-
 include: "rules/usvi.smk"
 include: "rules/prepare_sequences.smk"
 include: "rules/construct_phylogeny.smk"

diff --git a/phylogenetic/rules/annotate_phylogeny.smk b/phylogenetic/rules/annotate_phylogeny.smk
@@ -54,7 +54,7 @@ rule translate:
     input:
         tree = "results/tree.nwk",
         node_data = "results/nt_muts.json",
-        reference = files.reference
+        reference = "config/zika_reference.gb"
     output:
         node_data = "results/aa_muts.json"
     shell:

diff --git a/phylogenetic/rules/export.smk b/phylogenetic/rules/export.smk
@@ -34,9 +34,9 @@ rule export:
         traits = "results/traits.json",
         nt_muts = "results/nt_muts.json",
         aa_muts = "results/aa_muts.json",
-        colors = files.colors,
-        auspice_config = files.auspice_config,
-        description = files.description
+        colors = "config/colors.tsv",
+        auspice_config = "config/auspice_config.json",
+        description = "config/description.md"
     output:
         auspice_json = "results/raw_zika.json",
         root_sequence = "results/raw_zika_root-sequence.json",

diff --git a/phylogenetic/rules/prepare_sequences.smk b/phylogenetic/rules/prepare_sequences.smk
@@ -60,7 +60,7 @@ rule filter:
     input:
         sequences = "data/sequences_all.fasta",
         metadata = "data/metadata_all.tsv",
-        exclude = files.dropped_strains
+        exclude = "config/dropped_strains.txt",
     output:
         sequences = "results/filtered.fasta"
     params:
@@ -90,7 +90,7 @@ rule align:
     """
     input:
         sequences = "results/filtered.fasta",
-        reference = files.reference
+        reference = "config/zika_reference.gb"
     output:
         alignment = "results/aligned.fasta"
     shell: