add back regulatory

genomic-medicine-sweden · Oct 11, 2024 · d0d6049 · d0d6049
1 parent 00f48d2
commit d0d6049
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Showing 4 changed files with 18 additions and 20 deletions.
diff --git a/assets/svdb_query_vcf_schema.json b/assets/svdb_query_vcf_schema.json
@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/raredisease/master/assets/mobile_element_references_schema.json",
     "title": "Schema for SVDB query - VCF",
     "description": "Schema for the SVDB query database input, VCF version",

diff --git a/conf/modules/annotate_svs.config b/conf/modules/annotate_svs.config
@@ -34,7 +34,7 @@ process {
             '--exclude_predicted --force_overwrite --format vcf',
             '--hgvs --humdiv --max_sv_size 248387328',
             '--no_progress --numbers --per_gene --polyphen p',
-            '--protein --offline --sift p', // Add back regulatory with VEP 113
+            '--protein --offline --sift p --regulatory',
             '--symbol --tsl --uniprot --vcf',
             '--no_stats'
         ].join(' ') }

diff --git a/conf/test.config b/conf/test.config
@@ -10,14 +10,6 @@
 ----------------------------------------------------------------------------------------
 */
 
-process {
-    resourceLimits = [
-        cpus: 4,
-        memory: '15.GB',
-        time: '1.h'
-    ]
-}
-
 params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
@@ -60,7 +52,7 @@ params {
 
 // Impose same minimum Nextflow version as in nextflow.config
 manifest {
-    nextflowVersion = '!>=23.04.0'
+    nextflowVersion = '!>=24.04.2'
 }
 
 // Disable all Nextflow reporting options
@@ -70,16 +62,25 @@ trace    { enabled = false }
 dag      { enabled = false }
 
 process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
     withLabel: 'process_high' {
         cpus = 4
+        memory = '15.GB'
     }
     withLabel: 'process_medium' {
         cpus = 2
+        memory = '7.GB'
     }
     withLabel: 'process_low' {
         cpus = 1
+        memory = '3.GB'
     }
     withLabel: 'process_single' {
         cpus = 1
+        memory = '3.GB'
     }
 }
diff --git a/tests/nextflow.config b/tests/nextflow.config
@@ -5,14 +5,11 @@ params {
     // Base directory for genomic-medicine-sweden/nallo test data
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/7be7114cb132be8cae9343f225bcf42ec11ecc1b/'
 
-    max_cpus   = 4
-    max_memory = '15.GB'
-    max_time   = '6.h'
 }
 
 // Impose same minimum Nextflow version as the pipeline for testing
 manifest {
-    nextflowVersion = '!>=23.04.0'
+    nextflowVersion = '!>=24.04.2'
 }
 
 // Disable all Nextflow reporting options
@@ -22,25 +19,25 @@ trace    { enabled = false }
 dag      { enabled = false }
 
 process {
-
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
     withLabel: 'process_high' {
         cpus = 4
         memory = '15.GB'
     }
-
     withLabel: 'process_medium' {
         cpus = 2
         memory = '7.GB'
     }
-
     withLabel: 'process_low' {
         cpus = 1
         memory = '3.GB'
     }
-
     withLabel: 'process_single' {
         cpus = 1
         memory = '3.GB'
     }
-
 }