From 5edb7ce11289551706f95cb05bfbb6d731118d13 Mon Sep 17 00:00:00 2001
From: Finlay Maguire <finlaymaguire@gmail.com>
Date: Tue, 4 May 2021 16:30:27 -0300
Subject: [PATCH] Add optional configurable output directory for runs

---
 README.md                 |  5 +++++
 workflow/rules/common.smk | 12 ++++++++++++
 2 files changed, 17 insertions(+)

diff --git a/README.md b/README.md
index ffd1c27..4336262 100644
--- a/README.md
+++ b/README.md
@@ -139,6 +139,11 @@ completeness_threshold: 0.9
 # or the path to a local VCF file. 
 # Built in lists: https://github.com/jts/ncov-watch/tree/master/ncov_watch/watchlists
 mutation_set: spike_mutations
+
+# user specifiable output directory 
+# defaults to just current working directory but otherwise
+# will write output files to the specified directory
+output_directory: run1_output
 ```
 
 ## Running
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index a00704d..a67d34f 100644
--- a/workflow/rules/common.smk
+++ b/workflow/rules/common.smk
@@ -1,10 +1,22 @@
 #
 # Helper functions and rules
 #
+from pathlib import Path
+
 include: "defaults.smk"
 
 configfile: "config.yaml"
 
+# to handle custom output directories make input paths in config absolute
+# paths then assign snakemake workdir to the specified config workdir
+# as data_root is built into the remaining input paths
+if 'output_directory' in config:
+    for input_path_config in ['data_root', 'primer_bed', 'reference_genome', 'tree_include_consensus']:
+        if input_path_config in config:
+            config[input_path_config] = str(Path(config[input_path_config]).absolute())
+    workdir: config['output_directory']
+
+
 def get_sample_names():
 
     # if defined in the config, use that