Bump LolliPop 0.5.1

- avoids OpenBLAS threads explosion on clusters
- (extra pb option controlling the progress bars)

workflow/envs/lollipop.yaml

@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - lollipop =0.5.0
+  - lollipop =0.5.1

workflow/rules/signatures.smk

@@ -357,6 +357,7 @@ rule deconvolution:
         out_format=(
             "--fmt-columns" if config.deconvolution["out_format"] == "columns" else ""
         ),
+        EXTRA=config.deconvolution["extra"],
         seed="--seed=42",
     log:
         outfile=cohortdir("deconvoluted.out.log"),
@@ -372,7 +373,7 @@ 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} "--n-cores={threads}" "{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} {params.EXTRA} "--n-cores={threads}" "{input.tallymut}" 2> >(tee -a {log.errfile} >&2) > >(tee -a {log.outfile})
         """
 
 

workflow/schemas/config_schema.json

@@ -1687,6 +1687,12 @@
                     "default": "mut",
                     "description": "Timeline of events that deconvolution runs on.\n- `mut` simple mutations generated from basecounts (pile-up like)\n- `cooc` coocurrences of mutations on amplicons generated by COJAC",
                     "examples": ["cooc"]
+                },
+                "extra": {
+                    "type": "string",
+                    "default": "",
+                    "description": "Pass additional options to run `lollipop deconvolute` such as, e.g., `--bp` (see [LolliPop README](https://github.com/cbg-ethz/LolliPop)).",
+                    "examples": ["--bp 0"]
                 }
             },
             "default": {},