Add deepvariant_vcfstatsreport

genomic-medicine-sweden · Oct 29, 2024 · 1f0eee0 · 1f0eee0
1 parent 79b836b
commit 1f0eee0
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Showing 15 changed files with 1,024 additions and 107 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -27,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#430](https://github.com/genomic-medicine-sweden/nallo/pull/430) - Added a GitHub action to build and publish docs to GitHub Pages
 - [#431](https://github.com/genomic-medicine-sweden/nallo/pull/431) - Added files needed to automatically build and publish docs to GitHub Pages
 - [#435](https://github.com/genomic-medicine-sweden/nallo/pull/435) - Added nf-test to rank variants
+- [#](https://github.com/genomic-medicine-sweden/nallo/pull/) - Added the vcfstatsreport from DeepVariant to snv calling
 
 ### `Changed`
 

diff --git a/conf/modules/short_variant_calling.config b/conf/modules/short_variant_calling.config
@@ -43,6 +43,14 @@ process {
             meta.sex == 1 ? '--haploid_contigs="chrX,chrY"' : ''
         ].join(' ') }
     }
+    withName: '.*:SHORT_VARIANT_CALLING:DEEPVARIANT_VCFSTATSREPORT' {
+        publishDir = [
+            path: { "${params.outdir}/qc/deepvariant_vcfstatsreport/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+
+    }
 
     withName: '.*:SHORT_VARIANT_CALLING:GLNEXUS' {
         ext.args = '--config DeepVariant_unfiltered'
@@ -75,4 +83,5 @@ process {
             '-w 10000'
         ].join(' ')
     }
+
 }
diff --git a/docs/output.md b/docs/output.md
diff --git a/modules.json b/modules.json
@@ -80,6 +80,11 @@
                         "git_sha": "a7e8b8afd4fa82f20d745fa778bfdbf39c1f7efb",
                         "installed_by": ["modules"]
                     },
+                    "deepvariant/vcfstatsreport": {
+                        "branch": "master",
+                        "git_sha": "2f9a5431355897e299cb41928c45f51ea8410c42",
+                        "installed_by": ["modules"]
+                    },
                     "ensemblvep/vep": {
                         "branch": "master",
                         "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",

diff --git a/modules/nf-core/deepvariant/vcfstatsreport/main.nf b/modules/nf-core/deepvariant/vcfstatsreport/main.nf
diff --git a/modules/nf-core/deepvariant/vcfstatsreport/meta.yml b/modules/nf-core/deepvariant/vcfstatsreport/meta.yml
diff --git a/modules/nf-core/deepvariant/vcfstatsreport/tests/main.nf.test b/modules/nf-core/deepvariant/vcfstatsreport/tests/main.nf.test