Fix chewbbaca input link path

ssi-dk · Nov 14, 2024 · 704bb4a · 704bb4a
1 parent ef46743
commit 704bb4a
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Showing 2 changed files with 2 additions and 1 deletion.
diff --git a/bifrost_chewbbaca/pipeline.smk b/bifrost_chewbbaca/pipeline.smk
@@ -150,6 +150,7 @@ rule run_chewbbaca_on_genome:
         genome = rules.blast_gene_call.output.gene_calls
     output:
         chewbbaca_results = directory(f"{component['name']}/chewbbaca_results"),
+        results_tsv = f"{component['name']}/chewbbaca_results/output/results_alleles.tsv",
         chewbbaca_done = f"{component['name']}/chewbbaca_done"
     params:
         samplecomponent_ref_json = samplecomponent.to_reference().json,

diff --git a/bifrost_chewbbaca/rule__chewbbaca.py b/bifrost_chewbbaca/rule__chewbbaca.py
@@ -73,7 +73,7 @@ def __init__(self, sample_name, schema, genome, output, log):
     def prepare_run(self):
         self.inputdir = self.output / "input"
         self.inputdir.mkdir(parents=True)
-        Path(self.inputdir / (self.sample_name + ".fasta")).symlink_to(self.genome)
+        Path(self.inputdir / (self.sample_name + ".fasta")).symlink_to(self.genome.absolute())
 
     def run(self):
         cmd = [