update test_full

nf-core · Jan 15, 2025 · 120481c · 120481c
1 parent 4e71e74
commit 120481c
Showing 1 changed file with 36 additions and 21 deletions.
diff --git a/conf/test_full.config b/conf/test_full.config
@@ -14,28 +14,43 @@ params {
     config_profile_name        = 'Full test profile'
     config_profile_description = 'Full test dataset to check pipeline function'
 
-    // Input data for full size test
-    input           = params.pipelines_testdata_base_path + 'raredisease/testdata/samplesheet_full.csv'
-    intervals_wgs   = params.pipelines_testdata_base_path + 'raredisease/reference/test_full/genome.interval_list'
-    intervals_y     = params.pipelines_testdata_base_path + 'raredisease/reference/test_full/genomeY.interval_list'
-    target_bed      = params.pipelines_testdata_base_path + 'raredisease/reference/test_full/target.bed'
-    variant_catalog = params.pipelines_testdata_base_path + 'raredisease/reference/test_full/variant_catalog_hg38.json'
 
-    // Genome references
-    genome = 'GRCh38'
+    // reference params
+    igenomes_ignore = true
+    mito_name       = 'MT'
 
-    // Skip annotation
-    skip_mt_annotation  = true
-    skip_snv_annotation = true
-    skip_sv_annotation  = true
-}
+    // analysis params
+    skip_germlinecnvcaller = true
+    skip_peddy             = true
 
-process {
-    withName: 'MARKDUPLICATES' {
-        memory          = { check_max( 90.GB * task.attempt, 'memory' ) }
-    }
-    withName: 'DEEPVARIANT' {
-        cpus            = 24
-        memory          = { check_max( 90.GB * task.attempt, 'memory' ) }
-    }
+    // Input data
+    input          = params.pipelines_testdata_base_path + 'raredisease/testdata/samplesheet_trio.csv'
+
+    // Genome references
+    fasta                = params.pipelines_testdata_base_path + 'raredisease/reference/reference.fasta'
+    fai                  = params.pipelines_testdata_base_path + 'raredisease/reference/reference.fasta.fai'
+    genome               = 'GRCh37'
+    gnomad_af            = params.pipelines_testdata_base_path + 'raredisease/reference/gnomad_reformated.tab.gz'
+    intervals_wgs        = params.pipelines_testdata_base_path + 'raredisease/reference/target_wgs.interval_list'
+    intervals_y          = params.pipelines_testdata_base_path + 'raredisease/reference/targetY.interval_list'
+    known_dbsnp          = params.pipelines_testdata_base_path + 'raredisease/reference/dbsnp_-138-.vcf.gz'
+    ml_model             = 'https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.1.model'
+    mobile_element_references       = params.pipelines_testdata_base_path + 'raredisease/reference/mobile_element_references.tsv'
+    mobile_element_svdb_annotations = params.pipelines_testdata_base_path + 'raredisease/reference/svdb_querydb_files.csv'
+    reduced_penetrance   = params.pipelines_testdata_base_path + 'raredisease/reference/reduced_penetrance.tsv'
+    score_config_mt      = params.pipelines_testdata_base_path + 'raredisease/reference/rank_model_snv.ini'
+    score_config_snv     = params.pipelines_testdata_base_path + 'raredisease/reference/rank_model_snv.ini'
+    score_config_sv      = params.pipelines_testdata_base_path + 'raredisease/reference/rank_model_sv.ini'
+    svdb_query_dbs       = params.pipelines_testdata_base_path + 'raredisease/reference/svdb_querydb_files.csv'
+    target_bed           = params.pipelines_testdata_base_path + 'raredisease/reference/target.bed'
+    variant_catalog      = params.pipelines_testdata_base_path + 'raredisease/reference/variant_catalog.json'
+    vcfanno_lua          = params.pipelines_testdata_base_path + 'raredisease/reference/vcfanno_functions.lua'
+    vcfanno_resources    = params.pipelines_testdata_base_path + 'raredisease/reference/vcfanno_resources.txt'
+    vcfanno_toml         = params.pipelines_testdata_base_path + 'raredisease/reference/vcfanno_config.toml'
+    variant_consequences_snv = params.pipelines_testdata_base_path + 'raredisease/reference/variant_consequences_v2.txt'
+    variant_consequences_sv  = params.pipelines_testdata_base_path + 'raredisease/reference/variant_consequences_v2.txt'
+    vep_cache            = params.pipelines_testdata_base_path + 'raredisease/reference/vep_cache_and_plugins.tar.gz'
+    vep_filters          = params.pipelines_testdata_base_path + 'raredisease/reference/hgnc.txt'
+    vep_cache_version    = 107
+    vep_plugin_files     = params.pipelines_testdata_base_path + 'raredisease/reference/vep_files.csv'
 }