diff --git a/src/salmon.snake b/src/salmon.snake index 553c769..1a9d90d 100644 --- a/src/salmon.snake +++ b/src/salmon.snake @@ -13,7 +13,7 @@ rule salmon_index: input: REFERENCE_FASTA output: - join(config['dirs']['ref'], 'salmon', basename(REFERENCE_FASTA).rstrip(".fa")) + directory(join(config['dirs']['ref'], 'salmon', basename(REFERENCE_FASTA).rstrip(".fa"))) threads: 30 params: flags = config['salmon']['index_flags'] if 'index_flags' in config.get('salmon', {}) else ''