scripts.diff

 rules/config.smk | 22 ----------------------
 rules/genome.smk | 11 +++--------
 rules/main.smk   | 11 +++--------
 3 files changed, 6 insertions(+), 38 deletions(-)

diff --git a/rules/config.smk b/rules/config.smk
index 38cc55e..89ea2dd 100644
--- a/rules/config.smk
+++ b/rules/config.smk
@@ -179,28 +179,6 @@ def resolve_config_path(*fields):
 
     return resolve
 
-def script(path):
-    """
-    Resolve a provided script *path* (string)
-    
-    Search order (first match returned):
-        1. Relative to the 'scripts' directory in the avian-flu repo (`AVIAN_FLU_DIR`)
-        2. Relative to the avian-flu repo (`AVIAN_FLU_DIR`)
-
-    An `InvalidConfigError` is raised if a match is not found
-    """
-
-    if os.path.exists(p:=os.path.join(AVIAN_FLU_DIR, "scripts", path)):
-        return p
-    
-    if os.path.exists(p:=os.path.join(AVIAN_FLU_DIR, path)):
-        return p
-
-    raise InvalidConfigError(f"Unable to resolve the provided script {path!r}. "
-        f"The following directories were searched:\n"
-        f"\t1. {os.path.join(AVIAN_FLU_DIR, 'scripts')}\n"
-        f"\t2. {AVIAN_FLU_DIR}\n")
-
 
 def as_list(x):
     return x if isinstance(x, list) else [x]
diff --git a/rules/genome.smk b/rules/genome.smk
index 62d64c3..e8bb427 100644
--- a/rules/genome.smk
+++ b/rules/genome.smk
@@ -66,11 +66,9 @@ rule join_segments:
         subtype = 'h5n1-cattle-outbreak|h5n1-d1.1',
         segment = 'genome',
         time = 'default',
-    params:
-        script = script("join-segments.py"),
     shell:
         r"""
-        python {params.script} \
+        python {workflow.current_basedir}/../scripts/join-segments.py \
             --segments {input.alignment} \
             --output {output.alignment}
         """
@@ -82,14 +80,13 @@ rule mask_genome:
         alignment = "results/{subtype}/{segment}/{time}/aligned.fasta",
     params:
         percentage = resolve_config_value('mask', 'min_support'),
-        script = script("mask.py"),
     wildcard_constraints:
         subtype = 'h5n1-cattle-outbreak|h5n1-d1.1',
         segment = 'genome',
         time = 'default',
     shell:
         r"""
-        python {params.script} \
+        python {workflow.current_basedir}/../scripts/mask.py \
             --alignment {input.alignment} \
             --percentage {params.percentage} \
             --output {output.alignment}
@@ -153,11 +150,9 @@ rule prune_tree:
     wildcard_constraints:
         subtype='h5n1-cattle-outbreak|h5n1-d1.1',
         time="default",
-    params:
-        script = script("restrict-via-common-ancestor.py")
     shell:
         """
-        python3 {params.script} \
+        python {workflow.current_basedir}/../scripts/restrict-via-common-ancestor.py \
             --tree {input.tree} \
             --strains {input.strains} \
             --output-tree {output.tree} \
diff --git a/rules/main.smk b/rules/main.smk
index 5347e7e..183a6e5 100755
--- a/rules/main.smk
+++ b/rules/main.smk
@@ -270,11 +270,9 @@ rule add_h5_clade:
         clades_file = resolve_config_path('clades_file')
     output:
         metadata= "results/{subtype}/metadata-with-clade.tsv"
-    params:
-        script = script("clade-labeling/add-clades.py")
     shell:
         r"""
-        python {params.script} \
+        python {workflow.current_basedir}/../clade-labeling/add-clades.py \
             --metadata {input.metadata} \
             --output {output.metadata} \
             --clades {input.clades_file}
@@ -546,11 +544,9 @@ rule cleavage_site:
     output:
         cleavage_site_annotations = "results/{subtype}/ha/{time}/cleavage-site.json",
         cleavage_site_sequences = "results/{subtype}/ha/{time}/cleavage-site-sequences.json"
-    params:
-        script = script("annotate-ha-cleavage-site.py")
     shell:
         r"""
-        python {params.script} \
+        python {workflow.current_basedir}/../scripts/annotate-ha-cleavage-site.py \
             --alignment {input.alignment} \
             --furin_site_motif {output.cleavage_site_annotations} \
             --cleavage_site_sequence {output.cleavage_site_sequences}
@@ -633,11 +629,10 @@ rule colors:
         colors = "results/{subtype}/{segment}/{time}/colors.tsv",
     params:
         duplications = lambda w: ["=".join(pair) for pair in resolve_config_value('colors', 'duplications')(w)],
-        script = script("assign-colors.py"),
     shell:
         r"""
         cp {input.colors} {output.colors} && \
-        python3 {params.script} \
+        python {workflow.current_basedir}/../scripts/assign-colors.py \
             --metadata {input.metadata} \
             --ordering {input.ordering} \
             --color-schemes {input.schemes} \