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update plot pipeline with config file inputs #10

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merged 1 commit into from
Jul 15, 2024
Merged

update plot pipeline with config file inputs #10

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12 changes: 10 additions & 2 deletions association_testing/pipeline/plot.snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,13 @@
DEEPRVAT_ANALYSIS_DIR = os.environ['DEEPRVAT_ANALYSIS_DIR']
py_deeprvat_analysis = f'python {DEEPRVAT_ANALYSIS_DIR}'

configfile: 'deeprvat_config.yaml'

phenotypes = config['phenotypes']
phenotypes = list(phenotypes.keys()) if type(phenotypes) == dict else phenotypes
training_phenotypes = config["training"].get("phenotypes", phenotypes)
n_repeats = config['n_repeats']

rule plot:
conda:
"r-env"
Expand All @@ -13,11 +20,12 @@ rule plot:
phenotype=phenotypes),
replication = "replication.parquet"
output:
"dicovery_replication_plot.png"
"discovery_replication_plot.png"
params:
results_dir = './',
results_dir_pattern = '',
code_dir = f'{DEEPRVAT_ANALYSIS_DIR}/association_testing'
code_dir = f'{DEEPRVAT_ANALYSIS_DIR}/association_testing',
max_rank = 1000
resources:
mem_mb=20480,
load=16000,
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