Enable Parallel Deconvolution

cbg-ethz · Oct 11, 2024 · 59ce8c9 · 59ce8c9
1 parent 97cf46d
commit 59ce8c9
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Showing 3 changed files with 4 additions and 3 deletions.
diff --git a/workflow/envs/lollipop.yaml b/workflow/envs/lollipop.yaml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - lollipop =0.4.1
+  - lollipop =0.5.0
diff --git a/workflow/rules/signatures.smk b/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})
         """
 
 

diff --git a/workflow/schemas/config_schema.json b/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",