From 00ce5813a86c7d1548173818d6fd341710063666 Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Tue, 28 Jan 2025 10:43:16 +0100 Subject: [PATCH] fix: flag output directory with directory() Resolves error: ``` ImproperOutputException in rule prepare_nextclade in file /home/runner/work/ncov/ncov/workflow/snakemake_rules/main_workflow.smk, line 452: Outputs of incorrect type (directories when expecting files or vice versa). Output directories must be flagged with directory(). for rule prepare_nextclade: output: data/sars-cov-2-nextclade-defaults affected files: data/sars-cov-2-nextclade-defaults ``` https://github.com/nextstrain/ncov/actions/runs/13007476969/job/36277462988?pr=1170#step:8:136 --- workflow/snakemake_rules/main_workflow.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/snakemake_rules/main_workflow.smk b/workflow/snakemake_rules/main_workflow.smk index 9d4727d38..25db4f843 100644 --- a/workflow/snakemake_rules/main_workflow.smk +++ b/workflow/snakemake_rules/main_workflow.smk @@ -455,7 +455,7 @@ rule prepare_nextclade: Downloading reference files for nextclade (used for alignment and qc). """ output: - nextclade_dataset = "data/sars-cov-2-nextclade-defaults", + nextclade_dataset = directory("data/sars-cov-2-nextclade-defaults"), params: name = config["nextclade_dataset"], conda: config["conda_environment"]