add_dysgu_sarek

conf/modules/dysgu.config

@@ -0,0 +1,28 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    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.
+----------------------------------------------------------------------------------------
+*/
+
+// DYSGU
+
+process {
+    if (params.tools && params.tools.split(',').contains('dysgu')) {
+        withName: 'DYSGU_GERMLINE' {
+            ext.args   = { params.wes ? "--exome" : '' }
+            ext.prefix = { "${meta.id}.dysgu" }
+            publishDir = [
+                mode: params.publish_dir_mode,
+                path: { "${params.outdir}/variant_calling/dysgu/${meta.id}" },
+                pattern: "*{dysgu}.{vcf.gz,vcf.gz.tbi}"
+            ]
+        }
+    }
+}

modules.json

@@ -129,6 +129,11 @@
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/dragmap/hashtable/dragmap-hashtable.diff"
                     },
+                    "dysgu": {
+                        "branch": "master",
+                        "git_sha": "c27498285a0beca2239b395cf88129c586a837fc",
+                        "installed_by": ["modules"]
+                    },
                     "ensemblvep/download": {
                         "branch": "master",
                         "git_sha": "3db4f8488315cd7d7cf3fcb64251f6603210e831",

nextflow_schema.json

@@ -356,7 +356,7 @@
                 },
                 "cf_ploidy": {
                     "type": "string",
-                    "default": "2",
+                    "default": 2,
                     "fa_icon": "fas fa-bacon",
                     "help_text": "In case of doubt, you can set different values and Control-FREEC will select the one that explains most observed CNAs Example: ploidy=2 , ploidy=2,3,4. For more details, see the [manual](http://boevalab.inf.ethz.ch/FREEC/tutorial.html).",
                     "description": "Genome ploidy used by ControlFREEC",
@@ -1061,7 +1061,8 @@
                     "fa_icon": "far fa-check-circle",
                     "description": "Validation of parameters in lenient more.",
                     "hidden": true,
-                    "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
+                    "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode).",
+                    "default": true
                 },
                 "hook_url": {
                     "type": "string",