Use phylogenetic/scripts directory

nextstrain · Jul 8, 2024 · 12c35e4 · 12c35e4
1 parent cade1fe
commit 12c35e4
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Showing 6 changed files with 5 additions and 5 deletions.
diff --git a/nextclade/rules/export.smk b/nextclade/rules/export.smk
@@ -29,7 +29,7 @@ rule colors:
         colors = "results/colors_{serotype}.tsv"
     shell:
         """
-        python3 ../phylogenetic/bin/assign-colors.py \
+        python3 ../phylogenetic/scripts/assign-colors.py \
             --color-schemes {input.color_schemes} \
             --ordering {input.color_orderings} \
             --metadata {input.metadata} \
@@ -169,7 +169,7 @@ rule final_strain_name:
         display_strain_field=config.get("display_strain_field", "strain"),
     shell:
         """
-        python3 ../phylogenetic/bin/set_final_strain_name.py \
+        python3 ../phylogenetic/scripts/set_final_strain_name.py \
             --metadata {input.metadata} \
             --metadata-id-columns {params.strain_id} \
             --input-auspice-json {input.auspice_json} \

diff --git a/phylogenetic/rules/export.smk b/phylogenetic/rules/export.smk
@@ -29,7 +29,7 @@ rule colors:
         colors = "results/colors_{serotype}.tsv"
     shell:
         """
-        python3 bin/assign-colors.py \
+        python3 scripts/assign-colors.py \
             --color-schemes {input.color_schemes} \
             --ordering {input.color_orderings} \
             --metadata {input.metadata} \
@@ -171,7 +171,7 @@ rule final_strain_name:
         display_strain_field=config.get("display_strain_field", "strain"),
     shell:
         """
-        python3 bin/set_final_strain_name.py \
+        python3 scripts/set_final_strain_name.py \
             --metadata {input.metadata} \
             --metadata-id-columns {params.strain_id} \
             --input-auspice-json {input.auspice_json} \

diff --git a/phylogenetic/rules/prepare_sequences_E.smk b/phylogenetic/rules/prepare_sequences_E.smk
@@ -29,7 +29,7 @@ rule generate_E_reference_files:
         gene = "E",
     shell:
         """
-        python3 bin/newreference.py \
+        python3 scripts/newreference.py \
             --reference {input.reference} \
             --output-fasta {output.fasta} \
             --output-genbank {output.genbank} \

diff --git a/phylogenetic/bin/assign-colors.py → phylogenetic/scripts/assign-colors.py b/phylogenetic/bin/assign-colors.py → phylogenetic/scripts/assign-colors.py
diff --git a/phylogenetic/bin/newreference.py → phylogenetic/scripts/newreference.py b/phylogenetic/bin/newreference.py → phylogenetic/scripts/newreference.py
diff --git a/phylogenetic/bin/set_final_strain_name.py → ...ogenetic/scripts/set_final_strain_name.py b/phylogenetic/bin/set_final_strain_name.py → ...ogenetic/scripts/set_final_strain_name.py