From 12c35e4cda8fac96f5294e8cd8d45f5bd2cd1dfe Mon Sep 17 00:00:00 2001
From: Jennifer Chang <jennifer.chang.bioinform@gmail.com>
Date: Mon, 8 Jul 2024 14:31:25 -0400
Subject: [PATCH] Use phylogenetic/scripts directory

---
 nextclade/rules/export.smk                             | 4 ++--
 phylogenetic/rules/export.smk                          | 4 ++--
 phylogenetic/rules/prepare_sequences_E.smk             | 2 +-
 phylogenetic/{bin => scripts}/assign-colors.py         | 0
 phylogenetic/{bin => scripts}/newreference.py          | 0
 phylogenetic/{bin => scripts}/set_final_strain_name.py | 0
 6 files changed, 5 insertions(+), 5 deletions(-)
 rename phylogenetic/{bin => scripts}/assign-colors.py (100%)
 rename phylogenetic/{bin => scripts}/newreference.py (100%)
 rename phylogenetic/{bin => scripts}/set_final_strain_name.py (100%)

diff --git a/nextclade/rules/export.smk b/nextclade/rules/export.smk
index 7fab3156..35ca8427 100644
--- 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
index d2a8b930..c610eec3 100644
--- 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
index bf4f0b65..877fa304 100644
--- 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 b/phylogenetic/scripts/assign-colors.py
similarity index 100%
rename from phylogenetic/bin/assign-colors.py
rename to phylogenetic/scripts/assign-colors.py
diff --git a/phylogenetic/bin/newreference.py b/phylogenetic/scripts/newreference.py
similarity index 100%
rename from phylogenetic/bin/newreference.py
rename to phylogenetic/scripts/newreference.py
diff --git a/phylogenetic/bin/set_final_strain_name.py b/phylogenetic/scripts/set_final_strain_name.py
similarity index 100%
rename from phylogenetic/bin/set_final_strain_name.py
rename to phylogenetic/scripts/set_final_strain_name.py