edit: Use a permalink for each script

This would allow us to version the software we use in this workflow without being affected by upstream changes until we want to bump the version. This design adds more maintenance to this workflow, but it also protects users against unexpected issues that are outside of their control.

Discussed in nextstrain/ebola#6 (comment)

Snakefile

@@ -37,6 +37,7 @@ rule wrangle_metadata:
         metadata="results/wrangled_metadata.tsv",
     params:
         strain_id=lambda w: config.get("strain_id_field", "strain"),
+        wrangle_metadata_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/scripts/wrangle_metadata.py"
     shell:
         """
         if [[ ! -d bin ]]; then
@@ -253,7 +254,7 @@ rule final_strain_name:
         root_sequence="auspice/zika_root-sequence.json",
     params:
         display_strain_field=lambda w: config.get("display_strain_field", "strain"),
-        set_final_strain_name_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/scripts/set_final_strain_name.py",
+        set_final_strain_name_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/scripts/set_final_strain_name.py",
     shell:
         """
         if [[ ! -d bin ]]; then

ingest/workflow/snakemake_rules/fetch_sequences.smk

@@ -24,9 +24,9 @@ rule fetch_from_genbank:
         genbank_ndjson="data/genbank_{serotype}.ndjson",
     params:
         serotype_tax_id=download_serotype,
-        csv_to_ndjson_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/csv-to-ndjson",
-        fetch_from_genbank_url="https://raw.githubusercontent.com/nextstrain/dengue/new_ingest/ingest/bin/fetch-from-genbank",
-        genbank_url_url="https://raw.githubusercontent.com/nextstrain/dengue/new_ingest/ingest/bin/genbank-url", # Update if dengue merged
+        csv_to_ndjson_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/csv-to-ndjson",
+        fetch_from_genbank_url="https://raw.githubusercontent.com/nextstrain/dengue/ca659008bfbe4b3f799e11ecd106a0b95977fe93/ingest/bin/fetch-from-genbank",
+        genbank_url_url="https://raw.githubusercontent.com/nextstrain/dengue/ca659008bfbe4b3f799e11ecd106a0b95977fe93/ingest/bin/genbank-url", # Update if dengue merged
     shell:
         """
         if [[ ! -d bin ]]; then

ingest/workflow/snakemake_rules/slack_notifications.smk

@@ -28,7 +28,7 @@ rule notify_on_genbank_record_change:
         touch("data/notify/genbank-record-change.done"),
     params:
         s3_src=S3_SRC,
-        notify_on_record_change_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/notify-on-record-change",
+        notify_on_record_change_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/notify-on-record-change",
     shell:
         """
         if [[ ! -d bin ]]; then
@@ -52,7 +52,7 @@ rule notify_on_metadata_diff:
         touch("data/notify/metadata-diff.done"),
     params:
         s3_src=S3_SRC,
-        notify_on_diff_url = "https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/notify-on-diff",
+        notify_on_diff_url = "https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/notify-on-diff",
     shell:
         """
         if [[ ! -d bin ]]; then

ingest/workflow/snakemake_rules/transform.smk

@@ -62,15 +62,15 @@ rule transform:
         metadata_columns=config["transform"]["metadata_columns"],
         id_field=config["transform"]["id_field"],
         sequence_field=config["transform"]["sequence_field"],
-        transform_field_names_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/transform-field-names",
-        transform_string_fields_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/transform-string-fields",
-        transform_strain_names_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/transform-strain-names",
-        transform_date_fields_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/transform-date-fields",
-        transform_genbank_location_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/transform-genbank-location",
-        transform_authors_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/transform-authors",
-        apply_geolocation_rules_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/apply-geolocation-rules",
-        merge_user_metadata_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/merge-user-metadata",
-        ndjson_to_tsv_and_fasta_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/ndjson-to-tsv-and-fasta",
+        transform_field_names_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/transform-field-names",
+        transform_string_fields_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/transform-string-fields",
+        transform_strain_names_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/transform-strain-names",
+        transform_date_fields_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/transform-date-fields",
+        transform_genbank_location_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/transform-genbank-location",
+        transform_authors_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/transform-authors",
+        apply_geolocation_rules_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/apply-geolocation-rules",
+        merge_user_metadata_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/merge-user-metadata",
+        ndjson_to_tsv_and_fasta_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/ndjson-to-tsv-and-fasta",
     shell:
         """
         if [[ ! -d bin ]]; then

ingest/workflow/snakemake_rules/trigger_rebuild.smk

@@ -14,7 +14,7 @@ rule trigger_build:
     output:
         touch("data/trigger/rebuild.done")
     params:
-        trigger_on_new_data_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/trigger-on-new-data"
+        trigger_on_new_data_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/trigger-on-new-data"
     shell:
         """
         if [[ ! -d bin ]]; then

ingest/workflow/snakemake_rules/upload.smk

@@ -54,9 +54,9 @@ rule upload_to_s3:
         quiet="" if send_notifications else "--quiet",
         s3_dst=config["upload"].get("s3", {}).get("dst", ""),
         cloudfront_domain=config["upload"].get("s3", {}).get("cloudfront_domain", ""),
-        upload_to_s3_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/upload-to-s3",
-        sha256sum_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/sha256sum",
-        cloudfront_invalidate_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/cloudfront-invalidate"
+        upload_to_s3_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/upload-to-s3",
+        sha256sum_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/sha256sum",
+        cloudfront_invalidate_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/cloudfront-invalidate"
     shell:
         """
         if [[ ! -d bin ]]; then