From 59ce8c96e9080f697329bc72ca3a0a2fc4217a5b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gordon=20J=2E=20K=C3=B6hn?= <gordon@koehn.net>
Date: Fri, 11 Oct 2024 13:33:16 +0200
Subject: [PATCH] Enable Parallel Deconvolution

---
 workflow/envs/lollipop.yaml         | 2 +-
 workflow/rules/signatures.smk       | 2 +-
 workflow/schemas/config_schema.json | 3 ++-
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/workflow/envs/lollipop.yaml b/workflow/envs/lollipop.yaml
index a42daa39..4af3d5ce 100644
--- 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
index 7ae9fa01..55e0b96f 100644
--- 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
index fed024ea..00114f74 100644
--- 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",