From 704bb4a35416e7fb53060cb7a7879be6df807574 Mon Sep 17 00:00:00 2001 From: Kristoffer Kiil Date: Thu, 14 Nov 2024 20:19:01 +0100 Subject: [PATCH] Fix chewbbaca input link path --- bifrost_chewbbaca/pipeline.smk | 1 + bifrost_chewbbaca/rule__chewbbaca.py | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/bifrost_chewbbaca/pipeline.smk b/bifrost_chewbbaca/pipeline.smk index 19bb4b7..9a51114 100755 --- 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 index 13e4003..e252e9c 100755 --- 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 = [