Enable Parallel Deconvolution in Lollipop

workflow/envs/lollipop.yaml

@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - lollipop =0.4.1
+  - lollipop =0.5.0

workflow/rules/signatures.smk

@@ -362,7 +362,7 @@ rule deconvolution:
     threads: config.deconvolution["threads"]
     shell:
         """
-        {params.LOLLIPOP} deconvolute "--output={output.deconvoluted}" "--out-json={output.deconv_json}" "--var={input.var_conf}" "--vd={input.var_dates}" "--dec={input.deconv_conf}" "--filters={input.filters}" {params.out_format} {params.seed} "{input.tallymut}" 2> >(tee -a {log.errfile} >&2) > >(tee -a {log.outfile})
+        {params.LOLLIPOP} deconvolute "--output={output.deconvoluted}" "--out-json={output.deconv_json}" "--var={input.var_conf}" "--vd={input.var_dates}" "--dec={input.deconv_conf}" "--filters={input.filters}" {params.out_format} {params.seed} "--n-cores={threads}" "{input.tallymut}" 2> >(tee -a {log.errfile} >&2) > >(tee -a {log.outfile})
         """
 
 

workflow/schemas/config_schema.json

@@ -1630,7 +1630,8 @@
                 },
                 "threads": {
                     "type": "integer",
-                    "default": 4
+                    "default": 4,
+                    "description": "Cores for parallel processing for multiple locations, 1 for sequential processing"
                 },
                 "conda": {
                     "type": "string",