Resolve JSON paths

PathoGenOmics-Lab · Oct 11, 2023 · d69dc29 · d69dc29
1 parent ee70672
commit d69dc29
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/workflow/rules/evolution.smk b/workflow/rules/evolution.smk
@@ -4,8 +4,8 @@ rule N_S_sites:
     input:
         fasta = OUTDIR/f"{OUTPUT_NAME}.ancestor.fasta",
         gb = OUTDIR/"reference.gb",
-        features = config["FEATURES_JSON"],
-        genetic_code = config["GENETIC_CODE_JSON"]
+        features = Path(config["FEATURES_JSON"]).resolve(),
+        genetic_code = Path(config["GENETIC_CODE_JSON"]).resolve()
     output:
         csv = temp(OUTDIR/f"{OUTPUT_NAME}.ancestor.N_S.sites.csv")
     log:

diff --git a/workflow/rules/report.smk b/workflow/rules/report.smk
@@ -19,7 +19,7 @@ rule window:
     input:
         vcf = OUTDIR/f"{OUTPUT_NAME}.masked.filtered.tsv",
         gb = OUTDIR/"reference.gb",
-        features = config["FEATURES_JSON"]
+        features = Path(config["FEATURES_JSON"]).resolve()
     output:
         window_df = temp(OUTDIR/f"{OUTPUT_NAME}.window.csv"),
     log:

diff --git a/workflow/rules/vaf.smk b/workflow/rules/vaf.smk
@@ -59,7 +59,7 @@ rule annotation:
     input:
         gb = OUTDIR/"reference.gb",
         ref = OUTDIR/"reference.fasta",
-        features = config["FEATURES_JSON"]
+        features = Path(config["FEATURES_JSON"]).resolve()
     output:
         df = temp(OUTDIR/"annotation.csv")
     log: