Merge pull request #1180 from nextstrain/snakemake-v9

Snakemake v9 support

Author: joverlee521

.gitignore

@@ -8,6 +8,7 @@ auspice/
 data/*
 defaults/colors.tsv
 defaults/colors_*.tsv
+# stats.json was removed in Snakemake v8
 stats.json
 
 # common analysis directory names

Snakefile

@@ -7,12 +7,15 @@ from os import environ
 from socket import getfqdn
 from getpass import getuser
 from snakemake.logging import logger
-from snakemake.utils import validate
+from snakemake.utils import min_version, validate
 from collections import OrderedDict
 import textwrap
 import time
 
 
+# Minimum Snakemake version needed for the storage plugins used in remote_files.smk
+min_version("8.0.0")
+
 # Store the user's configuration prior to loading defaults, so we can check for
 # reused subsampling scheme names in the user's config. We need to make a deep
 # copy because Snakemake will deep merge the subsampling dictionary later,

docs/src/conf.py

@@ -126,6 +126,7 @@ def prose_list(items):
     # they block the client, probably anti-scraping measure
     r'^https://czgenepi\.org/resources',
     r'^https://science\.sciencemag\.org/content/early/2020/06/05/science\.abb9263',
+    r'^https://www\.medrxiv\.org',
     # this link is correct but the lack of a top-level dataset means
     # it 404s initially — because the point of this link is showing
     # the community page, allow it to fail here:

docs/src/reference/change_log.md

@@ -5,6 +5,14 @@ We also use this change log to document new features that maintain backward comp
 
 ## New features since last version update
 
+## v17 (17 July 2025)
+
+- 17 July 2025: Snakemake version 8 (or above) is now required. Various aspects of the workflow were incompatible with v8 including our support for remote files and have now been updated. The nextstrain runtimes have been correspondingly updated; see [the nextstrain-cli docs for how to upgrade these](https://docs.nextstrain.org/projects/cli/en/stable/commands/update/). [PR 1180](https://github.com/nextstrain/ncov/pull/1180)
+
+- 17 July 2025: Support for Google Cloud Storage via `path_or_url` has been removed. Please get in touch if this is needed as it should be possible to restore it. Implemented in [PR 1180](https://github.com/nextstrain/ncov/pull/1180) and discussed [in this zika PR](https://github.com/nextstrain/zika/pull/89#discussion_r2190671313).
+
+- 17 July 2025: Cluster support (both rhino and scicore) has been removed. [PR 1180](https://github.com/nextstrain/ncov/pull/1180)
+
 - 10 February 2025: Improve documentation regarding custom color map files.
 
 ## v16 (29 January 2025)

nextstrain_profiles/nextstrain-gisaid-21L/config.yaml

@@ -7,6 +7,4 @@ keep-going: False
 printshellcmds: True
 show-failed-logs: True
 restart-times: 2
-reason: True
-stats: stats.json
 set-threads: tree=4

nextstrain_profiles/nextstrain-gisaid/config.yaml

@@ -7,6 +7,4 @@ keep-going: False
 printshellcmds: True
 show-failed-logs: True
 restart-times: 2
-reason: True
-stats: stats.json
 set-threads: tree=4

nextstrain_profiles/nextstrain-open/config.yaml

@@ -7,6 +7,4 @@ keep-going: False
 printshellcmds: True
 show-failed-logs: True
 restart-times: 2
-reason: True
-stats: stats.json
 set-threads: tree=4