add_dysgu_sarek

conf/modules/dysgu.config

@@ -0,0 +1,26 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    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 {
+    withName: 'DYSGU' {
+        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: "*.{vcf.gz,vcf.gz.tbi}"
+        ]
+    }
+}

docs/output.md

@@ -45,6 +45,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
   - [Structural Variants](#structural-variants)
     - [Manta](#manta)
     - [TIDDIT](#tiddit)
+    - [DYSGU](#dysgu)
   - [Sample heterogeneity, ploidy and CNVs](#sample-heterogeneity-ploidy-and-cnvs)
     - [ASCAT](#ascat)
     - [CNVKit](#cnvkit)
@@ -639,6 +640,18 @@ It is optimized for analysis of germline variation in small sets of individuals
 
 </details>
 
+#### DYSGU
+
+[DYSGU](https://github.com/kcleal/dysgu) dysgu (pronounced duss-key) is a set of command line tools and python-API, for calling structural variants using paired-end or long read sequencing data. For further reading and documentation see the [DYSGU manual](https://github.com/kcleal/dysgu/blob/master/README.rst).
+
+<details markdown="1">
+<summary>Output files for normal samples</summary>
+
+**Output directory: `{outdir}/variantcalling/dysgu/<sample>/`**
+
+- `<sample>.dysgu.vcf.gz` and `<sample>.dysgu.vcf.gz.tbi`
+  - VCF with tabix index containing SV calls
+
 ### Sample heterogeneity, ploidy and CNVs
 
 #### ASCAT

modules.json

@@ -139,6 +139,11 @@
                         "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",