feat: add MuSE as new somatic variant caller

conf/modules/muse.config

@@ -0,0 +1,22 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+        ext.when   = When to run the module.
+----------------------------------------------------------------------------------------
+*/
+
+// MUSE
+
+process {
+
+    withName: 'MUSE_SUMP' {
+        ext.args   = { params.wes ? '-E' : '-G' }
+    }
+
+}

conf/test_full.config

@@ -18,7 +18,7 @@ params {
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/HCC1395_WXS_somatic_full_test.csv'
 
     // Other params
-    tools       = 'ngscheckmate,strelka,mutect2,freebayes,ascat,manta,cnvkit,tiddit,controlfreec,vep,snpeff'
+    tools       = 'ngscheckmate,strelka,mutect2,freebayes,ascat,manta,cnvkit,tiddit,controlfreec,vep,snpeff,muse'
     split_fastq = 20000000
     intervals   = 's3://ngi-igenomes/test-data/sarek/S07604624_Padded_Agilent_SureSelectXT_allexons_V6_UTR.bed'
     wes         = true

modules.json

@@ -349,6 +349,16 @@
                         "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
                     },
+                    "muse/call": {
+                        "branch": "master",
+                        "git_sha": "219299d7fc22a55cd3a07c2122044e7ca24b815f",
+                        "installed_by": ["modules"]
+                    },
+                    "muse/sump": {
+                        "branch": "master",
+                        "git_sha": "8e17f287034692420127d807c7631ae5ca4b9d0c",
+                        "installed_by": ["modules"]
+                    },
                     "ngscheckmate/ncm": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",