Fix wildcard issue

tdayris · Jul 16, 2024 · 78f5d1c · 78f5d1c
1 parent 50ac738
commit 78f5d1c
Showing 1 changed file with 5 additions and 5 deletions.
diff --git a/workflow/scripts/regenerate_genome.py b/workflow/scripts/regenerate_genome.py
@@ -74,26 +74,26 @@ def replace_col(df: pandas.DataFrame, column: str, default: str) -> pandas.DataF
 genomes = replace_col(
     df=genomes,
     column="dna_fasta",
-    default="reference/sequences/{species}.{build}.{reference}.dna/{species}.{build}.{release}.dna.fasta",
+    default="reference/sequences/{species}.{build}.{release}.dna/{species}.{build}.{release}.dna.fasta",
 )
 genomes = replace_col(
     df=genomes,
     column="dna_fai",
-    default="reference/sequences/{species}.{build}.{reference}.dna/{species}.{build}.{release}.dna.fasta.fai",
+    default="reference/sequences/{species}.{build}.{release}.dna/{species}.{build}.{release}.dna.fasta.fai",
 )
 genomes = replace_col(
     df=genomes,
     column="gtf",
-    default="reference/annotation/{species}.{build}.{reference}.dna/{species}.{build}.{release}.gtf",
+    default="reference/annotation/{species}.{build}.{release}.dna/{species}.{build}.{release}.gtf",
 )
 genomes = replace_col(
     df=genomes,
     column="genepred",
-    default="reference/annotation/{species}.{build}.{reference}.dna/{species}.{build}.{release}.genePred",
+    default="reference/annotation/{species}.{build}.{release}.dna/{species}.{build}.{release}.genePred",
 )
 genomes = replace_col(
     df=genomes,
     column="genepred_bed",
-    default="reference/annotation/{species}.{build}.{reference}.dna/{species}.{build}.{release}.genePred.bed",
+    default="reference/annotation/{species}.{build}.{release}.dna/{species}.{build}.{release}.genePred.bed",
 )
 genomes.to_csv(path_or_buf=snakemake.output.genomes, sep=",", header=True, index=False)