Merge pull request #523 from genomic-medicine-sweden/autozyg

chromograph autozyg
nf-core · Feb 29, 2024 · 7bf014f · 7bf014f
2 parents 9151e48 + e280515
commit 7bf014f
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Showing 3 changed files with 18 additions and 1 deletion.
diff --git a/conf/modules/annotate_rhocallviz.config b/conf/modules/annotate_rhocallviz.config
@@ -42,6 +42,17 @@ process {
         ]
     }
 
+    withName: '.*ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG' {
+        ext.prefix = { "${autozyg.simpleName}_autozyg_chromograph" }
+        ext.args = { "--euploid" }
+        ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample']).size() >= 1) || workflow.stubRun }
+        publishDir = [
+            path: { "${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" }

diff --git a/docs/output.md b/docs/output.md
@@ -402,6 +402,8 @@ Based on VEP annotations, custom scripts used by the pipeline further annotate e
   - `<case_id>_rohann_vcfanno_upd_sites_<chr#>.png`: file containing a plot showing upd sites across chromosomes.
 - `annotate_snv/genome/*regions_chromograph`
   - `<case_id>_rohann_vcfanno_upd_regions_<chr#>.png`: file containing a plot showing upd regions across chromosomes.
+- `annotate_snv/genome/*autozyg_chromograph`
+  - `<sample_id>_rhocallviz_<chr#>.png`: file containing a plot showing regions of autozygosity across chromosomes.
 
 </details>
 

diff --git a/subworkflows/local/annotation/annotate_rhocallviz.nf b/subworkflows/local/annotation/annotate_rhocallviz.nf
@@ -8,6 +8,7 @@ include { BCFTOOLS_ROH                              } from '../../../modules/nf-
 include { BCFTOOLS_VIEW as BCFTOOLS_VIEW_UNCOMPRESS } from '../../../modules/nf-core/bcftools/view/main'
 include { RHOCALL_VIZ                               } from '../../../modules/nf-core/rhocall/viz/main'
 include { UCSC_WIGTOBIGWIG                          } from '../../../modules/nf-core/ucsc/wigtobigwig/main'
+include { CHROMOGRAPH as CHROMOGRAPH_AUTOZYG        } from '../../../modules/nf-core/chromograph/main'
 
 workflow ANNOTATE_RHOCALLVIZ {
 
@@ -36,11 +37,14 @@ workflow ANNOTATE_RHOCALLVIZ {
 
         BCFTOOLS_VIEW_UNCOMPRESS(ch_roh_in,[],[],[])
 
-        RHOCALL_VIZ( BCFTOOLS_VIEW_UNCOMPRESS.out.vcf, BCFTOOLS_ROH.out.roh)
+        RHOCALL_VIZ(BCFTOOLS_VIEW_UNCOMPRESS.out.vcf, BCFTOOLS_ROH.out.roh)
+
+        CHROMOGRAPH_AUTOZYG(RHOCALL_VIZ.out.bed, [[],[]], [[],[]], [[],[]], [[],[]], [[],[]], [[],[]])
 
         UCSC_WIGTOBIGWIG(RHOCALL_VIZ.out.wig, ch_genome_chrsizes)
 
         ch_versions = ch_versions.mix(BCFTOOLS_VIEW.out.versions.first())
+        ch_versions = ch_versions.mix(CHROMOGRAPH_AUTOZYG.out.versions.first())
         ch_versions = ch_versions.mix(TABIX_TABIX.out.versions.first())
         ch_versions = ch_versions.mix(BCFTOOLS_ROH.out.versions.first())
         ch_versions = ch_versions.mix(BCFTOOLS_VIEW_UNCOMPRESS.out.versions.first())