Use scripts directory instead of bin #76

nextstrain · Jul 9, 2024 · 1a9ada3 · 1a9ada3
2 parents 011bea3 + 12c35e4
commit 1a9ada3
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Showing 13 changed files with 9 additions and 9 deletions.
diff --git a/ingest/README.md b/ingest/README.md
@@ -61,7 +61,7 @@ Do the following to include sequences from static FASTA files.
 1. Convert the FASTA files to NDJSON files with:
 
     ```sh
-    ./ingest/bin/fasta-to-ndjson \
+    ./ingest/scripts/fasta-to-ndjson \
         --fasta {path-to-fasta-file} \
         --fields {fasta-header-field-names} \
         --separator {field-separator-in-header} \

diff --git a/ingest/rules/curate.smk b/ingest/rules/curate.smk
@@ -93,12 +93,12 @@ rule curate:
                 --abbr-authors-field {params.abbr_authors_field} \
             | ./vendored/apply-geolocation-rules \
                 --geolocation-rules {input.all_geolocation_rules} \
-            | ./bin/infer-dengue-serotype.py \
+            | ./scripts/infer-dengue-serotype.py \
                 --out-col {params.serotype_field} \
             | ./vendored/merge-user-metadata \
                 --annotations {input.annotations} \
                 --id-field {params.annotations_id} \
-            | ./bin/ndjson-to-tsv-and-fasta \
+            | ./scripts/ndjson-to-tsv-and-fasta \
                 --metadata-columns {params.metadata_columns} \
                 --metadata {output.metadata} \
                 --fasta {output.sequences} \

diff --git a/ingest/rules/nextclade.smk b/ingest/rules/nextclade.smk
@@ -109,7 +109,7 @@ rule calculate_gene_coverage:
         serotype=SEROTYPE_CONSTRAINTS,
     shell:
         """
-        python bin/calculate-gene-converage-from-nextclade-translation.py \
+        python scripts/calculate-gene-converage-from-nextclade-translation.py \
           --fasta {input.nextclade_translation} \
           --out-col {wildcards.gene}_coverage \
           > {output.gene_coverage}

diff --git a/...e-converage-from-nextclade-translation.py → ...e-converage-from-nextclade-translation.py b/...e-converage-from-nextclade-translation.py → ...e-converage-from-nextclade-translation.py
diff --git a/ingest/bin/fasta-to-ndjson → ingest/scripts/fasta-to-ndjson b/ingest/bin/fasta-to-ndjson → ingest/scripts/fasta-to-ndjson
diff --git a/ingest/bin/infer-dengue-serotype.py → ingest/scripts/infer-dengue-serotype.py b/ingest/bin/infer-dengue-serotype.py → ingest/scripts/infer-dengue-serotype.py
diff --git a/ingest/bin/ndjson-to-tsv-and-fasta → ingest/scripts/ndjson-to-tsv-and-fasta b/ingest/bin/ndjson-to-tsv-and-fasta → ingest/scripts/ndjson-to-tsv-and-fasta
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