[bump] LolliPop 0.4.0

- support new `filters` option

workflow/envs/lollipop.yaml

@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - lollipop =0.3.0
+  - lollipop =0.4.0

workflow/rules/signatures.smk

@@ -320,6 +320,11 @@ rule deconvolution:
             if config.deconvolution["variants_dates"]
             else []
         ),
+        filters=(
+            config.deconvolution["filters"]
+            if config.deconvolution["filters"]
+            else []
+        ),
     output:
         deconvoluted=cohortdir("deconvoluted.tsv.zst"),
         deconv_json=cohortdir("deconvoluted_upload.json"),
@@ -343,7 +348,7 @@ 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}" {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} "{input.tallymut}" 2> >(tee -a {log.errfile} >&2) > >(tee -a {log.outfile})
         """
 
 

workflow/schemas/config_schema.json

@@ -1661,6 +1661,12 @@
                     "default": "lines",
                     "description": "Format of the output CSV.\n- `lines`(default) - each variants a separate entry on a separate line.\n- `columns` - one column per variant",
                     "examples": ["columns"]
+                },
+                "filters": {
+                    "type": "string",
+                    "default": "",
+                    "description": "List of filters for removing problematic mutations from tally. Some mutations might be problematic and need to be taken out -- e.g. due to drop-outs in the multiplex PCR amplification, they do not show up in the data and this could be misinterpreted by LolliPop as proof of absence of a variant.",
+                    "examples": ["filters_preprint.yaml"]
                 }
             },
             "default": {},