Merge pull request #67 from vinisalazar/dev

Merge branch `dev` into `main` - Metaphor v1.7.10
vinisalazar · Jan 15, 2024 · f2b817c · f2b817c
2 parents 05504a1 + 5977069
commit f2b817c
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Showing 4 changed files with 9 additions and 9 deletions.
diff --git 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"

diff --git 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}
     """
@@ -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")

diff --git 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}  

diff --git a/setup.py b/setup.py
@@ -32,18 +32,18 @@
         "pandas",
         "pyyaml",
         "requests",
-        "snakemake>=8",
+        "snakemake",
         "snakemake-wrapper-utils",
         "tqdm",
     ],
     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",
     ],
 )