feat: upgrade to use bgcflow wrapper v0.5.0 with use Snakemake v8.25.5

NBChub · Dec 5, 2024 · c9cb61c · c9cb61c
1 parent 7f2176b
commit c9cb61c
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Showing 6 changed files with 8 additions and 8 deletions.
diff --git a/.github/workflows/push.yml b/.github/workflows/push.yml
@@ -145,7 +145,7 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: 3.11
-      - run: pip install bgcflow_wrapper==0.4.0
+      - run: pip install "bgcflow_wrapper>=0.5.0"
       - run: pip install pytest-cov
       - run: pip install alive-progress
       - name: Test coverage

diff --git a/workflow/BGC b/workflow/BGC
@@ -186,7 +186,7 @@ wildcard_constraints:
 rule all:
     input:
         expand("data/processed/{name}/tables/df_gtdb_meta.csv", name=PROJECT_IDS),
-        get_final_output(DF_SAMPLES, PEP_PROJECTS, rule_dict_path="workflow/rules_bgc.yaml"),
+        get_final_output(DF_SAMPLES, PEP_PROJECTS, rule_dict_path="rules_bgc.yaml"),
 
 # Create place holder for resources defined in each modules, will be added if module is included, and passed to create custom_resource_dir
 resource_mapping = {}

diff --git a/workflow/Database b/workflow/Database
@@ -10,7 +10,7 @@ version = dependency_version["antismash"]
 
 ##### Make sure all required inputs exist
 NCBI = DF_SAMPLES[DF_SAMPLES.source.eq("ncbi")].genome_id.to_list()
-final_outputs = get_final_output(DF_SAMPLES, PEP_PROJECTS, rule_dict_path="workflow/rules.yaml", ignore_missing=True)
+final_outputs = get_final_output(DF_SAMPLES, PEP_PROJECTS, rule_dict_path="rules.yaml", ignore_missing=True)
 
 error_message = " * Has the jobs from the main workflow finished?\n * Check by running: 'bgcflow run -n'"
 for main_pipeline_outputs in final_outputs:

diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -49,7 +49,7 @@ wildcard_constraints:
 
 ##### Target rules #####
 
-final_outputs = get_final_output(DF_SAMPLES, PEP_PROJECTS, rule_dict_path="workflow/rules.yaml", ignore_missing=True)
+final_outputs = get_final_output(DF_SAMPLES, PEP_PROJECTS, rule_dict_path="rules.yaml", ignore_missing=True)
 
 rule all:
     input:

diff --git a/workflow/ppanggolin b/workflow/ppanggolin
@@ -51,7 +51,7 @@ wildcard_constraints:
 
 ##### Target rules #####
 
-final_outputs = get_final_output(DF_SAMPLES, PEP_PROJECTS, rule_dict_path="workflow/rules_ppanggolin.yaml", ignore_missing=True)
+final_outputs = get_final_output(DF_SAMPLES, PEP_PROJECTS, rule_dict_path="rules_ppanggolin.yaml", ignore_missing=True)
 
 rule all:
     input:

diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
@@ -8,8 +8,8 @@ from snakemake.utils import min_version
 from pathlib import Path
 import peppy
 
-min_version("7.14.0")
-__version__ = "1.1.2"
+min_version("8.25.5")
+__version__ = "1.2.0"
 
 
 container: "docker://matinnu/bgcflow:latest"
@@ -728,7 +728,7 @@ def get_project_outputs(
     Returns:
         final_output {list} -- list of final output files
     """
-    with open(workflow.source_path(f"../../{rule_dict_path}"), "r") as file:
+    with open(workflow.source_path(rule_dict_path), "r") as file:
         rule_dict = yaml.safe_load(file)
 
     selection = [