Merge pull request #80 from fmaguire/add_configurable_outputdir

Add configurable optional output directory

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

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