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fix patch - 0.7.9-1 #304

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merged 2 commits into from
Nov 28, 2023
Merged

fix patch - 0.7.9-1 #304

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df0ec9b
fix: use pandas unique instead of set
matinnuhamunada Nov 27, 2023
3bce639
chore: resolve internal paths using snakemake
matinnuhamunada Nov 28, 2023
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6 changes: 3 additions & 3 deletions workflow/rules/bgc_analytics.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ rule antismash_overview_gather:
bgc_overview=lambda wildcards: expand("data/interim/antismash/{version}/{strains}_bgc_overview.json",
name=wildcards.name,
version=wildcards.version,
strains=[s for s in set(PEP_PROJECTS[wildcards.name].sample_table.genome_id)],
strains=[s for s in PEP_PROJECTS[wildcards.name].sample_table.genome_id.unique()],
),
mapping_dir = "data/interim/bgcs/{name}/{version}",
output:
Expand Down Expand Up @@ -71,13 +71,13 @@ rule antismash_summary:
bgc_count=lambda wildcards: expand(
"data/interim/antismash/{version}/{strains}_bgc_counts.json",
version=wildcards.version,
strains=[s for s in set(PEP_PROJECTS[wildcards.name].sample_table.genome_id)],
strains=[s for s in PEP_PROJECTS[wildcards.name].sample_table.genome_id.unique()],
),
as_dir=lambda wildcards: expand(
"data/processed/{name}/antismash/{version}/{strains}",
name=wildcards.name,
version=wildcards.version,
strains=[s for s in set(PEP_PROJECTS[wildcards.name].sample_table.genome_id)],
strains=[s for s in PEP_PROJECTS[wildcards.name].sample_table.genome_id.unique()],
),
bgc_overview="data/processed/{name}/tables/df_regions_antismash_{version}.csv",
output:
Expand Down
13 changes: 7 additions & 6 deletions workflow/rules/common.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -346,14 +346,15 @@ def extract_project_information(config, project_variable="projects"):
)
# grab a bgcflow pep project
if p["name"].endswith(".yaml"):
pep_file = p["name"]
p = peppy.Project(p["name"], sample_table_index="genome_id")
assert len(workflow.configfiles) == 1, f"Only one config file is allowed. Found {workflow.configfiles}"
pep_file = Path(workflow.configfiles[0]).parent.parent / p["name"]
p = peppy.Project(str(pep_file), sample_table_index="genome_id")

# mask pipelines and rules as alias, use rules as default
if 'pipelines' in p.config.keys():
p.config['rules'] = p.config.pop("pipelines")

print(f" - Processing project [{p.name}]", file=sys.stderr)
print(f" - Processing project [{pep_file}]", file=sys.stderr)

# make sure each project has unique names
assert (
Expand Down Expand Up @@ -604,7 +605,8 @@ def get_dependency_version(dep, dep_key):
result {list} -- list of dependency version tags
"""
print(f"{dep_key} from: {dep[dep_key]}", file=sys.stderr)
with open(dep[dep_key]) as file:
conda_env_path = workflow.source_path(f"../../{dep[dep_key]}")
with open(conda_env_path) as file:
result = []
documents = yaml.full_load(file)
for i in documents["dependencies"]:
Expand Down Expand Up @@ -696,8 +698,7 @@ def get_project_outputs(
Returns:
final_output {list} -- list of final output files
"""

with open(rule_dict_path, "r") as file:
with open(workflow.source_path(f"../../{rule_dict_path}"), "r") as file:
rule_dict = yaml.safe_load(file)

selection = [
Expand Down