From 6d22388601988f069715b28d96bf1b81b2cfeac3 Mon Sep 17 00:00:00 2001
From: fellen31 <felixlenner@gmail.com>
Date: Wed, 14 Aug 2024 17:39:52 +0200
Subject: [PATCH] Keep SpliceAI in tests

---
 conf/modules/snv_annotation.config |  1 +
 conf/test.config                   | 20 ++++++++++++++++++++
 tests/nextflow.config              | 19 +++++++++++++++++++
 3 files changed, 40 insertions(+)

diff --git a/conf/modules/snv_annotation.config b/conf/modules/snv_annotation.config
index 36be4406..34e6748e 100644
--- a/conf/modules/snv_annotation.config
+++ b/conf/modules/snv_annotation.config
@@ -42,6 +42,7 @@ process {
             "--dir_plugins .",
             "--plugin LoFtool,LoFtool_scores.txt",
             "--plugin pLI,pLI_values.txt",
+            "--plugin SpliceAI,snv=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz,indel=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz",
             '--distance 5000',
             '--buffer_size 20000',
             '--format vcf --max_sv_size 248387328',
diff --git a/conf/test.config b/conf/test.config
index 62b7f114..8268f226 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -66,6 +66,26 @@ process {
         ext.args = '--gene hba'
     }
 
+    withName: '.*:SNV_ANNOTATION:ENSEMBLVEP_VEP' {
+        ext.prefix = { "${meta.id}_vep" }
+        ext.args = { [
+            "--dir_plugins .",
+            "--plugin LoFtool,LoFtool_scores.txt",
+            "--plugin pLI,pLI_values.txt",
+            "--plugin SpliceAI,snv=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz,indel=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz",
+            '--distance 5000',
+            '--buffer_size 20000',
+            '--format vcf --max_sv_size 248387328',
+            '--appris --biotype --cache --canonical --ccds --compress_output bgzip',
+            '--domains --exclude_predicted --force_overwrite',
+            '--hgvs --humdiv --no_progress --numbers',
+            '--polyphen p --protein --offline --regulatory --sift p --symbol --tsl',
+            '--uniprot --vcf',
+            '--no_stats'
+        ].join(' ') }
+    }
+
+    }
     withName: '.*:NALLO:PHASING:WHATSHAP_PHASE' {
         ext.args = '--ignore-read-groups --indels --distrust-genotypes --include-homozygous'
     }
diff --git a/tests/nextflow.config b/tests/nextflow.config
index 05f743ea..3c53747a 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -55,4 +55,23 @@ process {
         ext.args = '--ignore-read-groups --indels --distrust-genotypes --include-homozygous'
     }
 
+    withName: '.*:NALLO:SNV_ANNOTATION:ENSEMBLVEP_VEP' {
+        ext.prefix = { "${meta.id}_vep" }
+        ext.args = { [
+            "--dir_plugins .",
+            "--plugin LoFtool,LoFtool_scores.txt",
+            "--plugin pLI,pLI_values.txt",
+            "--plugin SpliceAI,snv=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz,indel=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz",
+            '--distance 5000',
+            '--buffer_size 20000',
+            '--format vcf --max_sv_size 248387328',
+            '--appris --biotype --cache --canonical --ccds --compress_output bgzip',
+            '--domains --exclude_predicted --force_overwrite',
+            '--hgvs --humdiv --no_progress --numbers',
+            '--polyphen p --protein --offline --regulatory --sift p --symbol --tsl',
+            '--uniprot --vcf',
+            '--no_stats'
+        ].join(' ') }
+    }
+
 }