Remove all use of message directive

Per Nextstrain's Snakemake style guide, using the `message` directive overrides the default Snakemake outputs which includes other critical details. <https://docs.nextstrain.org/en/latest/reference/snakemake-style-guide.html#avoid-the-message-rule-attribute>
nextstrain · Jun 17, 2024 · eb63e29 · eb63e29
1 parent 5be2a53
commit eb63e29
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Showing 3 changed files with 12 additions and 20 deletions.
diff --git a/workflow/snakemake_rules/fetch_sequences.smk b/workflow/snakemake_rules/fetch_sequences.smk
@@ -126,8 +126,7 @@ rule create_genbank_ndjson:
         """
 
 rule fetch_biosample:
-    message:
-        """Fetching BioSample data (GenBank only)"""
+    """Fetching BioSample data (GenBank only)"""
     output:
         biosample = temp("data/biosample.ndjson")
     benchmark:
@@ -140,8 +139,7 @@ rule fetch_biosample:
 
 
 rule fetch_cog_uk_accessions:
-    message:
-        """Fetching COG-UK sample accesions (GenBank only)"""
+    """Fetching COG-UK sample accesions (GenBank only)"""
     output:
         cog_uk_accessions = temp("data/cog_uk_accessions.tsv")
     benchmark:
@@ -154,8 +152,7 @@ rule fetch_cog_uk_accessions:
 
 
 rule fetch_cog_uk_metadata:
-    message:
-        """Fetching COG-UK metadata (GenBank only)"""
+    """Fetching COG-UK metadata (GenBank only)"""
     output:
         cog_uk_metadata = temp("data/cog_uk_metadata.csv.gz")
     benchmark:
@@ -243,8 +240,7 @@ if config.get("s3_dst") and config.get("s3_src"):
         ruleorder: fetch_main_ndjson_from_s3 > create_genbank_ndjson
 
     rule fetch_main_ndjson_from_s3:
-        message:
-            """Fetching main NDJSON from AWS S3"""
+        """Fetching main NDJSON from AWS S3"""
         params:
             file_on_s3_dst=f"{config['s3_dst']}/{database}.ndjson.zst",
             file_on_s3_src=f"{config['s3_src']}/{database}.ndjson.zst",
@@ -260,8 +256,7 @@ if config.get("s3_dst") and config.get("s3_src"):
             """
 
     rule fetch_biosample_from_s3:
-        message:
-            """Fetching BioSample NDJSON from AWS S3"""
+        """Fetching BioSample NDJSON from AWS S3"""
         params:
             file_on_s3_dst=f"{config['s3_dst']}/biosample.ndjson.zst",
             file_on_s3_src=f"{config['s3_src']}/biosample.ndjson.zst",

diff --git a/workflow/snakemake_rules/nextclade.smk b/workflow/snakemake_rules/nextclade.smk
@@ -34,17 +34,15 @@ wildcard_constraints:
 
 
 rule create_empty_nextclade_info:
-    message:
-        """Creating empty NextClade info cache file"""
+    """Creating empty NextClade info cache file"""
     output:
         touch(f"data/{database}/nextclade{{reference}}_old.tsv"),
     benchmark:
         f"benchmarks/create_empty_nextclade_info_{database}{{reference}}.txt"
 
 
 rule create_empty_nextclade_aligned:
-    message:
-        """Creating empty NextClade aligned cache file"""
+    """Creating empty NextClade aligned cache file"""
     output:
         touch(f"data/{database}/nextclade.aligned.old.fasta"),
         *[
@@ -277,10 +275,9 @@ rule nextclade_tsv_concat_versions:
 
 
 rule nextclade_info:
-    message:
-        """
-        Generates nextclade info TSV for all sequences (new + old)
-        """
+    """
+    Generates nextclade info TSV for all sequences (new + old)
+    """
     input:
         old_info=f"data/{database}/nextclade{{reference}}_old.tsv",
         new_info=rules.nextclade_tsv_concat_versions.output.tsv,

diff --git a/workflow/snakemake_rules/trigger.smk b/workflow/snakemake_rules/trigger.smk
@@ -12,7 +12,7 @@ These output files are empty flag files to force Snakemake to run the trigger ru
 """
 
 rule trigger_rebuild_pipeline:
-    message: "Triggering nextstrain/ncov rebuild action (via repository dispatch)"
+    """Triggering nextstrain/ncov rebuild action (via repository dispatch)"""
     input:
         metadata_upload = f"data/{database}/metadata.tsv.zst.upload",
         fasta_upload = f"data/{database}/aligned.fasta.zst.upload",
@@ -32,7 +32,7 @@ rule trigger_rebuild_pipeline:
         """
 
 rule trigger_counts_pipeline:
-    message: "Triggering nextstrain/counts clade counts action (via repository dispatch)"
+    """Triggering nextstrain/counts clade counts action (via repository dispatch)"""
     input:
         f"data/{database}/upload.done"
     output: