From b80b4b945806f0d74ea50f8aa05bbe6c6311818e Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Mon, 15 Jan 2024 12:07:54 +1100
Subject: [PATCH 1/5] Use single hyphen to detect 'skip_report' args

---
 metaphor/cli/execute.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/metaphor/cli/execute.py b/metaphor/cli/execute.py
index fb8ff54..f00a484 100644
--- a/metaphor/cli/execute.py
+++ b/metaphor/cli/execute.py
@@ -114,8 +114,8 @@ def main(args):
     get_successful_completion(retcode, msg)
 
     # Don't run report if running unlock, lint or cleanup metadata option
-    options = ["unlock", "lint", "cleanup-metadata", "dry-run", "dryrun"]
-    skip_report = True if any(f"--{o}" in cmd for o in options) else skip_report
+    options = ["unlock", "lint", "cleanup-metadata", "dry-run", "dryrun", "n"]
+    skip_report = True if any(f"--{o}" in cmd for o in options) or any(f"-{o}" in cmd for o in options) else skip_report
 
     if not skip_report:
         timestamp = datetime.now().strftime("%Y-%m-%dT%H:%M:%S")

From bcc2c21de149c2a1bab13a6603e215b5d12e97b0 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Mon, 15 Jan 2024 12:09:15 +1100
Subject: [PATCH 2/5] Bump version

  - Bump Snakemake-wrappers version
---
 metaphor/__init__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/metaphor/__init__.py b/metaphor/__init__.py
index 13a3651..59b2527 100644
--- a/metaphor/__init__.py
+++ b/metaphor/__init__.py
@@ -2,7 +2,7 @@
 __email__ = "17276653+vinisalazar@users.noreply.github.com"
 __license__ = "MIT"
 __copyright__ = "The University of Melbourne 2023"
-__version__ = "1.7.9"
+__version__ = "1.7.10"
 
 __doc__ = """
 Metaphor top-level module. This is the entrypoint for the `cli`, `config`, and `workflow` packages.
@@ -13,7 +13,7 @@
 
 # Snakemake wrapper version
 # This should match the latest released tag on: https://github.com/snakemake/snakemake-wrappers
-wrapper_version = "v2.6.0"
+wrapper_version = "v3.3.3"
 wrapper_prefix = "https://github.com/snakemake/snakemake-wrappers/raw/"
 
 github_url = "https://github.com/vinisalazar/metaphor"

From 04303fa1e350b112d643ace23432e2c138e32916 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Mon, 15 Jan 2024 12:15:32 +1100
Subject: [PATCH 3/5] Remove '-r' argument from Snakemake command

  This argument is now always on by default on Snakemake 8.
---
 metaphor/cli/execute.py | 2 +-
 metaphor/cli/test.py    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/metaphor/cli/execute.py b/metaphor/cli/execute.py
index f00a484..2163136 100644
--- a/metaphor/cli/execute.py
+++ b/metaphor/cli/execute.py
@@ -84,7 +84,7 @@ def main(args):
     snakemake --snakefile {snakefile}           \
               --configfile {config_file}        \
               --cores {cores}                   \
-              -p -r                             \
+              --printshellcmds                  \
               --use-conda                       \
               --wrapper-prefix {wrapper_prefix}
     """
diff --git a/metaphor/cli/test.py b/metaphor/cli/test.py
index 38b03a3..f0948d9 100644
--- a/metaphor/cli/test.py
+++ b/metaphor/cli/test.py
@@ -142,7 +142,7 @@ def main(args):
     snakemake --snakefile {snakefile}           \
               --configfile {test_config}        \
               --cores {cores}                   \
-              -p -r                             \
+              --printshellcmds                  \
               --use-conda                       \
               --wrapper-prefix {wrapper_prefix} \
               --conda-prefix {conda_prefix}  

From 937a833175824368f817bdd4593fc797dfd68a7d Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Mon, 15 Jan 2024 12:17:28 +1100
Subject: [PATCH 4/5] Remove dependency pin for Snakemake

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 06cc871..06cd9f9 100644
--- a/setup.py
+++ b/setup.py
@@ -32,7 +32,7 @@
         "pandas",
         "pyyaml",
         "requests",
-        "snakemake>=8",
+        "snakemake",
         "snakemake-wrapper-utils",
         "tqdm",
     ],

From 5977069a280346e888ba9ea343379e7236201632 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Mon, 15 Jan 2024 12:18:28 +1100
Subject: [PATCH 5/5] Relax Python dependency requirements

---
 setup.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index 06cd9f9..abce4a2 100644
--- a/setup.py
+++ b/setup.py
@@ -38,12 +38,12 @@
     ],
     extras_require={"docs": "myst_parser"},
     keywords="metagenomics binning assembly snakemake workflow pipeline",
-    python_requires=">=3.11",
+    python_requires=">=3.9",
     classifiers=[
         "Development Status :: 3 - Alpha",
         "Intended Audience :: Science/Research",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
         "License :: OSI Approved :: MIT License",
-        "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.9",
     ],
 )