From a086a497b46f36a6827caf9b20a1e9a12506b03a Mon Sep 17 00:00:00 2001
From: Jover Lee <joverlee521@gmail.com>
Date: Mon, 17 Jun 2024 11:29:29 -0700
Subject: [PATCH 1/4] fetch-and-ingest: Add Snakemake `--stats` output

Adding as part of #240 to help collect more data for tackling #446.

One unexpected behavior that I ran into when testing the `--stats`
option is that Snakemake doesn't generate the stats file if the
workflow exits with an error at any step.

Note that the Snakemake `--stats` option is not available starting with
Snakemake v8, so this will need to be removed when we eventually
upgrade Snakemake in our runtimes.
---
 .github/workflows/fetch-and-ingest-genbank-master.yml | 1 +
 .github/workflows/fetch-and-ingest-gisaid-master.yml  | 1 +
 2 files changed, 2 insertions(+)

diff --git a/.github/workflows/fetch-and-ingest-genbank-master.yml b/.github/workflows/fetch-and-ingest-genbank-master.yml
index 1fad4f00..1419c810 100644
--- a/.github/workflows/fetch-and-ingest-genbank-master.yml
+++ b/.github/workflows/fetch-and-ingest-genbank-master.yml
@@ -108,5 +108,6 @@ jobs:
           --env SLACK_CHANNELS \
           --env PAT_GITHUB_DISPATCH="$GH_TOKEN_NEXTSTRAIN_BOT_WORKFLOW_DISPATCH" \
           . \
+            --stats snakemake_stats.json \
             --configfile config/genbank.yaml \
             $CONFIG_OVERRIDES
diff --git a/.github/workflows/fetch-and-ingest-gisaid-master.yml b/.github/workflows/fetch-and-ingest-gisaid-master.yml
index babbb6c1..3c811bb0 100644
--- a/.github/workflows/fetch-and-ingest-gisaid-master.yml
+++ b/.github/workflows/fetch-and-ingest-gisaid-master.yml
@@ -109,5 +109,6 @@ jobs:
           --env SLACK_CHANNELS \
           --env PAT_GITHUB_DISPATCH="$GH_TOKEN_NEXTSTRAIN_BOT_WORKFLOW_DISPATCH" \
           . \
+            --stats snakemake_stats.json \
             --configfile config/gisaid.yaml \
             $CONFIG_OVERRIDES

From 185cd9cbe6de840d9ec3b394c4ce3b09279a5e50 Mon Sep 17 00:00:00 2001
From: Jover Lee <joverlee521@gmail.com>
Date: Mon, 17 Jun 2024 15:56:41 -0700
Subject: [PATCH 2/4] Add benchmark to all Snakemake rules

Adding as part of #240 to help collect more data for tackling #446.
---
 workflow/snakemake_rules/curate.smk           | 10 +++++++
 workflow/snakemake_rules/fetch_sequences.smk  | 28 +++++++++++++++++++
 workflow/snakemake_rules/nextclade.smk        | 22 +++++++++++++++
 .../snakemake_rules/slack_notifications.smk   |  6 ++++
 workflow/snakemake_rules/trigger.smk          |  4 +++
 workflow/snakemake_rules/upload.smk           |  6 ++++
 6 files changed, 76 insertions(+)

diff --git a/workflow/snakemake_rules/curate.smk b/workflow/snakemake_rules/curate.smk
index 5d1dfe64..75b65f48 100644
--- a/workflow/snakemake_rules/curate.smk
+++ b/workflow/snakemake_rules/curate.smk
@@ -29,6 +29,8 @@ rule transform_rki_data:
     output:
         fasta="data/rki_sequences.fasta",
         metadata="data/rki_metadata_transformed.tsv",
+    benchmark:
+        "benchmarks/transform_rki_data.txt"
     params:
         subsampled=config.get("subsampled", False),
     shell:
@@ -45,6 +47,8 @@ rule transform_biosample:
         biosample = "data/biosample.ndjson"
     output:
         biosample = "data/genbank/biosample.tsv"
+    benchmark:
+        "benchmarks/transform_biosample.txt"
     shell:
         """
         ./bin/transform-biosample {input.biosample} \
@@ -85,6 +89,8 @@ rule merge_open_data:
     output:
         metadata="data/genbank/metadata_transformed.tsv",
         sequences="data/genbank/sequences.fasta",
+    benchmark:
+        "benchmarks/merge_open_data.txt"
     shell:
         """
         ./bin/merge-open \
@@ -105,6 +111,8 @@ rule transform_gisaid_data:
         metadata = "data/gisaid/metadata_transformed.tsv",
         flagged_annotations = temp("data/gisaid/flagged-annotations"),
         additional_info = "data/gisaid/additional_info.tsv"
+    benchmark:
+        "benchmarks/transform_gisaid_data.txt"
     shell:
         """
         ./bin/transform-gisaid {input.ndjson} \
@@ -120,6 +128,8 @@ rule flag_metadata:
         metadata = "data/gisaid/metadata.tsv"
     output:
         metadata = "data/gisaid/flagged_metadata.txt"
+    benchmark:
+        "benchmarks/flag_metadata.txt"
     resources:
         # Memory use scales primarily with the size of the metadata file.
         mem_mb=20000
diff --git a/workflow/snakemake_rules/fetch_sequences.smk b/workflow/snakemake_rules/fetch_sequences.smk
index 1926ed07..f460bb0a 100644
--- a/workflow/snakemake_rules/fetch_sequences.smk
+++ b/workflow/snakemake_rules/fetch_sequences.smk
@@ -21,6 +21,8 @@ Produces different final outputs for GISAID vs GenBank/RKI:
 rule fetch_main_gisaid_ndjson:
     output:
         ndjson = temp(f"data/gisaid.ndjson")
+    benchmark:
+        "benchmarks/fetch_main_gisaid_ndjson.txt"
     retries: 5
     shell:
         """
@@ -128,6 +130,8 @@ rule fetch_biosample:
         """Fetching BioSample data (GenBank only)"""
     output:
         biosample = temp("data/biosample.ndjson")
+    benchmark:
+        "benchmarks/fetch_biosample.txt"
     retries: 5
     shell:
         """
@@ -140,6 +144,8 @@ rule fetch_cog_uk_accessions:
         """Fetching COG-UK sample accesions (GenBank only)"""
     output:
         cog_uk_accessions = temp("data/cog_uk_accessions.tsv")
+    benchmark:
+        "benchmarks/fetch_cog_uk_accessions.txt"
     retries: 5
     shell:
         """
@@ -152,6 +158,8 @@ rule fetch_cog_uk_metadata:
         """Fetching COG-UK metadata (GenBank only)"""
     output:
         cog_uk_metadata = temp("data/cog_uk_metadata.csv.gz")
+    benchmark:
+        "benchmarks/fetch_cog_uk_metadata.txt"
     retries: 5
     shell:
         """
@@ -164,6 +172,8 @@ rule uncompress_cog_uk_metadata:
         "data/cog_uk_metadata.csv.gz"
     output:
         cog_uk_metadata = temp("data/cog_uk_metadata.csv")
+    benchmark:
+        "benchmarks/uncompress_cog_uk_metadata.txt"
     shell:
         "gunzip -c {input} > {output}"
 
@@ -171,6 +181,8 @@ rule uncompress_cog_uk_metadata:
 rule fetch_rki_sequences:
     output:
         rki_sequences=temp("data/rki_sequences.fasta.xz"),
+    benchmark:
+        "benchmarks/fetch_rki_sequences.txt"
     retries: 5
     shell:
         """
@@ -181,6 +193,8 @@ rule fetch_rki_sequences:
 rule fetch_rki_metadata:
     output:
         rki_metadata=temp("data/rki_metadata.tsv.xz"),
+    benchmark:
+        "benchmarks/fetch_rki_metadata.txt"
     retries: 5
     shell:
         """
@@ -194,6 +208,8 @@ rule transform_rki_data_to_ndjson:
         rki_metadata="data/rki_metadata.tsv.xz"
     output:
         ndjson="data/rki.ndjson",
+    benchmark:
+        "benchmarks/transform_rki_data_to_ndjson.txt"
     shell:
         """
         ./bin/transform-rki-data-to-ndjson \
@@ -235,6 +251,8 @@ if config.get("s3_dst") and config.get("s3_src"):
             lines = config.get("subsample",{}).get("main_ndjson", 0)
         output:
             ndjson = temp(f"data/{database}.ndjson")
+        benchmark:
+            "benchmarks/fetch_main_ndjson_from_s3.txt"
         shell:
             """
             ./vendored/download-from-s3 {params.file_on_s3_dst} {output.ndjson} {params.lines} ||  \
@@ -250,6 +268,8 @@ if config.get("s3_dst") and config.get("s3_src"):
             lines = config.get("subsample",{}).get("biosample", 0)
         output:
             biosample = temp("data/biosample.ndjson")
+        benchmark:
+            "benchmarks/fetch_biosample_from_s3.txt"
         shell:
             """
             ./vendored/download-from-s3 {params.file_on_s3_dst} {output.biosample} {params.lines} ||  \
@@ -263,6 +283,8 @@ if config.get("s3_dst") and config.get("s3_src"):
             lines = config.get("subsample",{}).get("rki_ndjson", 0)
         output:
             rki_ndjson = temp("data/rki.ndjson")
+        benchmark:
+            "benchmarks/fetch_rki_ndjson_from_s3.txt"
         shell:
             """
             ./vendored/download-from-s3 {params.file_on_s3_dst} {output.rki_ndjson} {params.lines} ||  \
@@ -275,6 +297,8 @@ if config.get("s3_dst") and config.get("s3_src"):
             lines = config.get("subsample",{}).get("cog_uk_accessions", 0)
         output:
             biosample = "data/cog_uk_accessions.tsv" if config.get("keep_temp",False) else temp("data/cog_uk_accessions.tsv")
+        benchmark:
+            "benchmarks/fetch_cog_uk_accessions_from_s3.txt"
         shell:
             """
             ./vendored/download-from-s3 {params.file_on_s3_dst} {output.biosample} {params.lines} ||  \
@@ -288,6 +312,8 @@ if config.get("s3_dst") and config.get("s3_src"):
             lines = config.get("subsample",{}).get("cog_uk_metadata", 0)
         output:
             biosample = temp("data/cog_uk_metadata.csv")
+        benchmark:
+            "benchmarks/fetch_cog_uk_metadata_from_s3.txt"
         shell:
             """
             ./vendored/download-from-s3 {params.file_on_s3_dst} {output.biosample} {params.lines} ||  \
@@ -299,5 +325,7 @@ if config.get("s3_dst") and config.get("s3_src"):
             "data/cog_uk_metadata.csv"
         output:
             cog_uk_metadata = "data/cog_uk_metadata.csv.gz" if config.get("keep_temp",False) else temp("data/cog_uk_metadata.csv.gz")
+        benchmark:
+            "benchmarks/compress_cog_uk_metadata.txt"
         shell:
             "gzip -c {input} > {output}"
diff --git a/workflow/snakemake_rules/nextclade.smk b/workflow/snakemake_rules/nextclade.smk
index c31077c0..a0a5a047 100644
--- a/workflow/snakemake_rules/nextclade.smk
+++ b/workflow/snakemake_rules/nextclade.smk
@@ -40,6 +40,8 @@ rule create_empty_nextclade_info:
         """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:
@@ -51,6 +53,8 @@ rule create_empty_nextclade_aligned:
             touch(f"data/{database}/nextclade.translation_{gene}.old.fasta")
             for gene in GENE_LIST
         ],
+    benchmark:
+        f"benchmarks/create_empty_nextclade_aligned_{database}.txt"
 
 
 # Only include rules to fetch from S3 if S3 config params are provided
@@ -74,6 +78,8 @@ if config.get("s3_dst") and config.get("s3_src"):
             lines=config.get("subsample", {}).get("nextclade", 0),
         output:
             nextclade=f"data/{database}/nextclade{{reference}}_old.tsv",
+        benchmark:
+            f"benchmarks/download_nextclade_tsv_from_s3_{database}{{reference}}.txt"
         shell:
             """
             ./vendored/download-from-s3 {params.dst_rerun_touchfile} {output.nextclade} 0 ||  \
@@ -95,6 +101,8 @@ if config.get("s3_dst") and config.get("s3_src"):
             lines=config.get("subsample", {}).get("nextclade", 0),
         output:
             alignment=temp(f"data/{database}/nextclade.{{seqtype}}.old.fasta"),
+        benchmark:
+            f"benchmarks/download_previous_alignment_from_s3_{database}{{seqtype}}.txt"
         shell:
             """
             ./vendored/download-from-s3 {params.dst_rerun_touchfile} {output.alignment} 0 ||  \
@@ -132,6 +140,8 @@ rule download_nextclade_executable:
     """Download Nextclade"""
     output:
         nextclade="nextclade",
+    benchmark:
+        f"benchmarks/download_nextclade_executable_{database}.txt"
     shell:
         """
         if [ "$(uname)" = "Darwin" ]; then
@@ -158,6 +168,8 @@ rule download_nextclade_dataset:
         "nextclade",
     output:
         dataset="data/nextclade_data/{dataset_name}.zip",
+    benchmark:
+        f"benchmarks/download_nextclade_dataset_{database}_{{dataset_name}}.txt"
     shell:
         """
         ./nextclade dataset get --name="{wildcards.dataset_name}" --output-zip={output.dataset} --verbose
@@ -185,6 +197,8 @@ rule run_wuhan_nextclade:
             temp(f"data/{database}/nextclade.translation_{gene}.upd.fasta")
             for gene in GENE_LIST
         ],
+    benchmark:
+        f"benchmarks/run_wuhan_nextclade_{database}.txt"
     shell:
         """
         # If there are no sequences to run Nextclade on, create empty output files
@@ -214,6 +228,8 @@ rule run_21L_nextclade:
         sequences=f"data/{database}/nextclade_21L.sequences.fasta",
     output:
         info=f"data/{database}/nextclade_21L_new_raw.tsv",
+    benchmark:
+        f"benchmarks/run_21L_nextclade_{database}.txt"
     shell:
         """
         # If there are no sequences to run Nextclade on, create empty output files
@@ -235,6 +251,8 @@ rule nextclade_tsv_concat_versions:
         dataset=lambda w: f"data/nextclade_data/sars-cov-2{w.reference.replace('_','-')}.zip",
     output:
         tsv=f"data/{database}/nextclade{{reference}}_new.tsv",
+    benchmark:
+        f"benchmarks/nextclade_tsv_concat_versions_{database}{{reference}}.txt"
     shell:
         """
         if [ -s {input.tsv} ]; then
@@ -270,6 +288,8 @@ rule nextclade_info:
         new_info=rules.nextclade_tsv_concat_versions.output.tsv,
     output:
         nextclade_info=f"data/{database}/nextclade{{reference}}.tsv",
+    benchmark:
+        f"benchmarks/nextclade_info_{database}{{reference}}.txt"
     shell:
         """
         tsv-append -H {input.old_info} {input.new_info} \
@@ -286,6 +306,8 @@ rule combine_alignments:
         new_alignment=f"data/{database}/nextclade.{{seqtype}}.upd.fasta",
     output:
         alignment=f"data/{database}/{{seqtype}}.fasta",
+    benchmark:
+        f"benchmarks/combine_alignments_{database}{{seqtype}}.txt"
     params:
         keep_temp=config.get("keep_temp", "false"),
     shell:
diff --git a/workflow/snakemake_rules/slack_notifications.smk b/workflow/snakemake_rules/slack_notifications.smk
index 5fe52eb6..4687cb6e 100644
--- a/workflow/snakemake_rules/slack_notifications.smk
+++ b/workflow/snakemake_rules/slack_notifications.smk
@@ -30,6 +30,8 @@ rule notify_on_record_change:
         ndjson_on_s3 = f"{config['s3_src']}/{database}.ndjson.xz"
     output:
         touch(f"data/{database}/notify-on-record-change.done")
+    benchmark:
+        f"benchmarks/notify_on_record_change_{database}.txt"
     shell:
         """
         ./vendored/notify-on-record-change {input.ndjson} {params.ndjson_on_s3} {database}
@@ -46,6 +48,8 @@ rule notify_gisaid:
         s3_bucket = config["s3_src"]
     output:
         touch("data/gisaid/notify.done")
+    benchmark:
+        "benchmarks/notify_gisaid.txt"
     run:
         shell("./vendored/notify-slack --upload flagged-annotations < {input.flagged_annotations}")
         shell("./bin/notify-on-additional-info-change {input.additional_info} {params.s3_bucket}/additional_info.tsv.gz")
@@ -60,6 +64,8 @@ rule notify_genbank:
         s3_bucket = config["s3_src"]
     output:
         touch("data/genbank/notify.done")
+    benchmark:
+        "benchmarks/notify_genbank.txt"
     run:
         shell("./vendored/notify-slack --upload flagged-annotations < {input.flagged_annotations}")
         # TODO - which rule produces data/genbank/problem_data.tsv? (was not explicit in `ingest-genbank` bash script)
diff --git a/workflow/snakemake_rules/trigger.smk b/workflow/snakemake_rules/trigger.smk
index 49937a6a..e56fe8f5 100644
--- a/workflow/snakemake_rules/trigger.smk
+++ b/workflow/snakemake_rules/trigger.smk
@@ -18,6 +18,8 @@ rule trigger_rebuild_pipeline:
         fasta_upload = f"data/{database}/aligned.fasta.zst.upload",
     output:
         touch(f"data/{database}/trigger-rebuild.done")
+    benchmark:
+        f"benchmarks/trigger_rebuild_pipeline_{database}.txt"
     params:
         dispatch_type = f"{database}/rebuild"
     shell:
@@ -35,6 +37,8 @@ rule trigger_counts_pipeline:
         f"data/{database}/upload.done"
     output:
         touch(f"data/{database}/trigger-counts.done")
+    benchmark:
+        f"benchmarks/trigger_counts_pipeline_{database}.txt"
     params:
         dispatch_type = f"{database}/clade-counts"
     shell:
diff --git a/workflow/snakemake_rules/upload.smk b/workflow/snakemake_rules/upload.smk
index 2002cbf5..2b8a02bb 100644
--- a/workflow/snakemake_rules/upload.smk
+++ b/workflow/snakemake_rules/upload.smk
@@ -87,6 +87,8 @@ rule upload_single:
         notifications_flag = f"data/{database}/notify.done" if send_notifications else [],
     output:
         "data/{database}/{remote_filename}.upload",
+    benchmark:
+        "benchmarks/upload_single_{database}_{remote_filename}.txt"
     params:
         quiet = "" if send_notifications else "--quiet",
         s3_bucket = config.get("s3_dst",""),
@@ -108,6 +110,8 @@ rule remove_rerun_touchfile:
         f"data/{database}/{{remote_filename}}.upload",
     output:
         f"data/{database}/{{remote_filename}}.renew.deleted",
+    benchmark:
+        f"benchmarks/remove_rerun_touchfile_{database}_{{remote_filename}}.txt"
     params:
         dst_rerun_touchfile=config["s3_dst"] + "/{remote_filename}.renew",
     shell:
@@ -131,3 +135,5 @@ rule upload:
         ]
     output:
         touch(f"data/{database}/upload.done")
+    benchmark:
+        f"benchmarks/upload_{database}.txt"

From 5be2a53466d623baaac7a44baa63638ef47f453a Mon Sep 17 00:00:00 2001
From: Jover Lee <joverlee521@gmail.com>
Date: Mon, 17 Jun 2024 15:58:24 -0700
Subject: [PATCH 3/4] nextclade.smk: remove unused import

The use of `shellquote` was removed in 2dab1f94f1478fe100283f0a26607e3a7aa84bb5.
---
 workflow/snakemake_rules/nextclade.smk | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/workflow/snakemake_rules/nextclade.smk b/workflow/snakemake_rules/nextclade.smk
index a0a5a047..a4a861d2 100644
--- a/workflow/snakemake_rules/nextclade.smk
+++ b/workflow/snakemake_rules/nextclade.smk
@@ -27,8 +27,6 @@ Produces the following outputs:
         alignment = f"data/{database}/aligned.fasta"
 """
 
-from shlex import quote as shellquote
-
 
 wildcard_constraints:
     reference="|_21L",
@@ -158,7 +156,7 @@ rule download_nextclade_executable:
         fi
 
         NEXTCLADE_VERSION="$(./nextclade --version)"
-        echo "[ INFO] Nextclade version: $NEXTCLADE_VERSION" 
+        echo "[ INFO] Nextclade version: $NEXTCLADE_VERSION"
         """
 
 

From eb63e2954f6286c0de5c0804bf58c8e3ccd12b44 Mon Sep 17 00:00:00 2001
From: Jover Lee <joverlee521@gmail.com>
Date: Mon, 17 Jun 2024 16:02:15 -0700
Subject: [PATCH 4/4] 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>
---
 workflow/snakemake_rules/fetch_sequences.smk | 15 +++++----------
 workflow/snakemake_rules/nextclade.smk       | 13 +++++--------
 workflow/snakemake_rules/trigger.smk         |  4 ++--
 3 files changed, 12 insertions(+), 20 deletions(-)

diff --git a/workflow/snakemake_rules/fetch_sequences.smk b/workflow/snakemake_rules/fetch_sequences.smk
index f460bb0a..7ba24804 100644
--- 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
index a4a861d2..8d24c236 100644
--- a/workflow/snakemake_rules/nextclade.smk
+++ b/workflow/snakemake_rules/nextclade.smk
@@ -34,8 +34,7 @@ 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:
@@ -43,8 +42,7 @@ rule create_empty_nextclade_info:
 
 
 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
index e56fe8f5..e4b7ce99 100644
--- 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: