Merge pull request nf-core#512 from genomic-medicine-sweden/rhocall_viz

Add rhocall viz

conf/modules/annotate_mobile_elements.config

@@ -54,7 +54,7 @@ process {
 
     withName: '.*ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER' {
         // extend filter with arguments such as --exclude 'INFO/swegen_sva_FRQ > 0.1'
-        ext.args = { "--apply-filters PASS" }
+        ext.args = { "--apply-filters PASS --output-type z" }
         ext.prefix = { "${meta.id}_filter" }
     }
 

conf/modules/annotate_rhocallviz.config

@@ -0,0 +1,54 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    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            = Conditional clause
+----------------------------------------------------------------------------------------
+*/
+
+//
+// rhocall viz options
+//
+
+process {
+
+    withName: '.*ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW' {
+        ext.prefix = { "${meta.sample}" }
+        ext.args   = { "--output-type z --min-ac 1 --samples ${meta.sample}" }
+    }
+
+    withName: '.*ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH' {
+        ext.prefix = { "${meta.sample}" }
+        ext.args   = { "--AF-tag GNOMADAF --skip-indels" }
+    }
+
+    withName: '.*ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS' {
+        ext.prefix = { "${meta.sample}" }
+        ext.args   = { "--output-type v" }
+    }
+
+    withName: '.*ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ' {
+        ext.prefix = { "${meta.sample}_rhocallviz" }
+        ext.args   = { "--aftag GNOMADAF --wig" }
+        publishDir = [
+            path: { "${params.outdir}/annotate_snv/genome" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: '.*ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG' {
+        ext.prefix = { "${meta.sample}_rhocallviz" }
+        ext.args   = { "-clip" }
+        publishDir = [
+            path: { "${params.outdir}/annotate_snv/genome/${meta.sample}_rhocallviz" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+}

docs/output.md

@@ -52,6 +52,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
       - [VEP](#vep)
       - [UPD](#upd)
       - [Chromograph](#chromograph)
+      - [Rhocall viz](#rhocall-viz)
     - [Annotation - SV](#annotation---sv)
       - [SVDB query](#svdb-query)
       - [VEP](#vep-1)
@@ -403,6 +404,19 @@ Based on VEP annotations, custom scripts used by the pipeline further annotate e
 
 </details>
 
+#### Rhocall viz
+
+[Rhocall viz](https://github.com/dnil/rhocall) plots binned zygosity and RHO-regions.
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `annotate_snv/genome/<sample_id>_rhocallviz/<sample_id>_rhocallviz.bed`: file containing regions of homozygosity in bed format.
+- `annotate_snv/genome/<sample_id>_rhocallviz/<sample_id>_rhocallviz.wig`: file containing the fraction of homozygous SNPs in wig format.
+- `annotate_snv/genome/<sample_id>_rhocallviz/<sample_id>_rhocallviz.bw`: file containing the fraction of homozygous SNPs in bigwig format.
+
+</details>
+
 ### Annotation - SV
 
 #### SVDB query

modules.json

@@ -47,7 +47,7 @@
                     },
                     "bcftools/view": {
                         "branch": "master",
-                        "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
+                        "git_sha": "1013101da4252623fd7acf19cc581bae91d4f839",
                         "installed_by": ["modules"]
                     },
                     "bedtools/genomecov": {
@@ -358,6 +358,11 @@
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
+                    "rhocall/viz": {
+                        "branch": "master",
+                        "git_sha": "1013101da4252623fd7acf19cc581bae91d4f839",
+                        "installed_by": ["modules"]
+                    },
                     "rtgtools/format": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",