feat: CLIN-3610 introduce nf-core vep subworkflow

Ferlab-Ste-Justine · Dec 20, 2024 · 5d9569f · 5d9569f
1 parent ea8a954
commit 5d9569f
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Showing 17 changed files with 632 additions and 59 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -72,7 +72,6 @@ process {
 
     withName: ENSEMBLVEP_VEP {
         container = 'ensemblorg/ensembl-vep:release_111.0' //sticking to v111 for now, but we should update this
-        publishDir = new_publish_dir([enabled: true])
         def args_list =  [
             "--offline",
             "--format vcf",
@@ -92,12 +91,13 @@ process {
         ext.prefix =  {"variants.${meta.id}.vep"}
     }
 
+    withName: '.*VCF_ANNOTATE_ENSEMBLVEP.*' {
+        publishDir = new_publish_dir([enabled: true, path: { "${params.outdir}/ensemblvep" }])
+    }
+
     // To publish the vep index file in the same output folder as the vep output
-    withName: 'vep_tabix' {
-        publishDir = new_publish_dir([
-            enabled: true,
-            path: { "${params.outdir}/ensemblvep" }
-        ])
+    withName: TABIX_TABIX {
+        container = 'staphb/htslib:1.20'
     }
 
     withName: 'splitMultiAllelics' {

diff --git a/modules.json b/modules.json
@@ -23,7 +23,7 @@
           "ensemblvep/vep": {
             "branch": "master",
             "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4",
-            "installed_by": ["modules"]
+            "installed_by": ["modules", "vcf_annotate_ensemblvep"]
           },
           "gatk4/genotypegvcfs": {
             "branch": "master",
@@ -34,6 +34,11 @@
             "branch": "master",
             "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
             "installed_by": ["modules"]
+          },
+          "tabix/tabix": {
+            "branch": "master",
+            "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+            "installed_by": ["vcf_annotate_ensemblvep"]
           }
         }
       },
@@ -53,6 +58,11 @@
             "branch": "master",
             "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
             "installed_by": ["subworkflows"]
+          },
+          "vcf_annotate_ensemblvep": {
+            "branch": "master",
+            "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+            "installed_by": ["subworkflows"]
           }
         }
       }

diff --git a/modules/local/tabix.nf b/modules/local/tabix.nf
diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml
diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf
diff --git a/modules/nf-core/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml
diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test