refactor: get log dir paths from config

zavolanlab · Sep 6, 2023 · 0042a78 · 0042a78
1 parent 6a37a8a
commit 0042a78
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/tests/test_htsinfer_workflow/test.local.sh b/tests/test_htsinfer_workflow/test.local.sh
@@ -36,6 +36,8 @@ snakemake \
     --config outdir="results" \
              samples="../input_files/htsinfer_samples.tsv" \
              samples_out="samples_htsinfer.tsv" \
+             log_dir="logs" \
+             cluster_log_dir="logs/cluster_log" \
     --notemp \
     --keep-incomplete
 
diff --git a/workflow/rules/htsinfer.smk b/workflow/rules/htsinfer.smk
@@ -12,8 +12,8 @@ samples = pd.read_csv(
     config["samples"], header=0, index_col=0, sep="\t", keep_default_na=False
 )
 OUT_DIR = config["outdir"]
-LOG_DIR = os.path.join(OUT_DIR, "logs")
-CLUSTER_LOG = os.path.join(LOG_DIR, "cluster_logs")
+LOG_DIR = config["log_dir"]
+CLUSTER_LOG = config["cluster_log_dir"]
 # Write inferred params into new sample table.
 SAMPLES_OUT = os.path.join(OUT_DIR, config["samples_out"])