From 151128188532c364b23f3f369aa9fe29e99397c7 Mon Sep 17 00:00:00 2001 From: Tom Kasper Date: Thu, 17 Sep 2026 22:26:44 +0100 Subject: [PATCH] typo fix for all rule, fixed f-string handling in dorado model folder helper --- workflow/Snakefile | 2 +- workflow/rules/baseline_pipeline.smk | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/workflow/Snakefile b/workflow/Snakefile index 72ead89..7363fb6 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -25,7 +25,7 @@ rule all: #'../data/raw_pod5/' #'../data/pod5_files_to_pull', #'../data/basecalled_reads/hac.fastq.gz' - expand('../data/raw_pod5/PBK98658_853a956f_57f83f46_{batch}.fastq.gz',batch=range(1,config["pod5_dataset_size"]+1,config["pod5_stride"])) + expand('../data/raw_pod5/PBK98658_853a956f_57f83f46_{batch}.pod5',batch=range(1,config["pod5_dataset_size"]+1,config["pod5_stride"])) use rule * from preparation use rule * from baseline diff --git a/workflow/rules/baseline_pipeline.smk b/workflow/rules/baseline_pipeline.smk index f46d762..2cdc07e 100644 --- a/workflow/rules/baseline_pipeline.smk +++ b/workflow/rules/baseline_pipeline.smk @@ -3,7 +3,8 @@ def get_model_name(wildcards): return config[config_param] def get_model_requirement(wildcards): - return f"{config['dorado_model_dir']}/{config[f'{wildcards.model}_model_name']} + config_param=f'{wildcards.model}_model_name' + return config['dorado_model_dir']+'/'+config[config_param] def get_benchmarking_file(wildcards): config_param = f'{wildcards.model}_benchmarks_file'