From 31e72fb3c4516e16959e7a7feccddb3544e7261c Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Thu, 17 Aug 2023 11:07:24 +0200
Subject: [PATCH] add sentieon config

---
 conf/test.config          |  7 -----
 conf/test_sentieon.config | 59 +++++++++++++++++++++++++++++++++++++++
 nextflow.config           |  1 +
 3 files changed, 60 insertions(+), 7 deletions(-)
 create mode 100644 conf/test_sentieon.config

diff --git a/conf/test.config b/conf/test.config
index 9093bfb6..8065aa8a 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -50,10 +50,3 @@ params {
     vep_filters          = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt"
     vep_cache_version    = 107
 }
-
-process {
-    withLabel: 'sentieon' {
-        ext.sentieon_auth_mech_base64 = secrets.SENTIEON_AUTH_MECH_BASE64
-        ext.sentieon_auth_data_base64 = secrets.SENTIEON_AUTH_DATA_BASE64
-    }
-}
diff --git a/conf/test_sentieon.config b/conf/test_sentieon.config
new file mode 100644
index 00000000..9093bfb6
--- /dev/null
+++ b/conf/test_sentieon.config
@@ -0,0 +1,59 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/raredisease -profile test,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus       = 2
+    max_memory     = '6.GB'
+    max_time       = '2.h'
+
+    // reference params
+    igenomes_ignore = true
+    mito_name       = 'MT'
+
+    // analysis params
+    skip_cnv_calling = true
+
+    // Input data
+    input          = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_trio.csv'
+
+    // Genome references
+    fasta                = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta"
+    genome               = 'GRCh37'
+    gnomad_af            = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz"
+    intervals_wgs        = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list"
+    intervals_y          = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list"
+    known_dbsnp          = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz"
+    ml_model             = "https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.0.model"
+    reduced_penetrance   = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv"
+    score_config_snv     = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini"
+    score_config_sv      = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini"
+    svdb_query_dbs       = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv"
+    target_bed           = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed"
+    variant_catalog      = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json"
+    vcfanno_lua          = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua"
+    vcfanno_resources    = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt"
+    vcfanno_toml         = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml"
+    vep_cache            = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz"
+    vep_filters          = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt"
+    vep_cache_version    = 107
+}
+
+process {
+    withLabel: 'sentieon' {
+        ext.sentieon_auth_mech_base64 = secrets.SENTIEON_AUTH_MECH_BASE64
+        ext.sentieon_auth_data_base64 = secrets.SENTIEON_AUTH_DATA_BASE64
+    }
+}
diff --git a/nextflow.config b/nextflow.config
index 185940df..2ec6a4df 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -196,6 +196,7 @@ profiles {
     test            { includeConfig 'conf/test.config'            }
     test_full       { includeConfig 'conf/test_full.config'       }
     test_one_sample { includeConfig 'conf/test_one_sample.config' }
+    test_sentieon   { includeConfig 'conf/test_sentieon.config'            }
 }
 
 // Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile