From ffe6a9a2b4b353c0cf447a18b1ab9d45e8dcad2b Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 15 Sep 2022 11:47:44 +0200
Subject: [PATCH] use complete selectors to gain priority over
 conf/modules.config

---
 conf/test.config | 36 ++++++++++++++++++++++++++++++++++++
 nextflow.config  |  6 ------
 2 files changed, 36 insertions(+), 6 deletions(-)

diff --git a/conf/test.config b/conf/test.config
index 1e1bae8816..dc64ff820b 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -51,6 +51,42 @@ params {
     schema_ignore_params = 'genomes,test_data,snpeff_version,vep_version'
 }
 
+process {
+    withName:'.*:FREEC_SOMATIC'{
+        ext.args = {
+            [
+                "sample":[
+                    inputformat: "pileup",
+                    mateorientation: "FR"
+                ],
+                "general":[
+                    bedgraphoutput: "TRUE",
+                    noisydata: "TRUE",
+                    minexpectedgc: "0",
+                    readcountthreshold: "1",
+                    sex: meta.sex,
+                    window: "10",
+                    ],
+                "control":[
+                    inputformat: "pileup",
+                    mateorientation: "FR"
+                ]
+            ]
+        }
+    }
+
+    if (params.tools && params.tools.split(',').contains('mutect2')) {
+        withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING:MUTECT2'{
+            //sample name from when the test data was generated
+            ext.args = { "--f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz --normal-sample normal " }
+        }
+    }
+
+    withName: '.*:FILTERVARIANTTRANCHES'{
+        ext.args = { "--info-key CNN_1D --indel-tranche 0" }
+    }
+}
+
 // Enable container engines/virtualisation envs for CI testing
 // only works when specified with the profile ENV
 // otherwise tests can be done with the regular provided profiles
diff --git a/nextflow.config b/nextflow.config
index 2d85f6e9d9..337e58c684 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -283,12 +283,6 @@ manifest {
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules.config'
 
-// Include extra DSL2 module specific options for tests after loading conf/modules.config to avoid conflicts
-profiles {
-    tools_somatic       { includeConfig 'conf/test_tools_somatic_modules.config' }
-    tools_somatic_ascat { includeConfig 'conf/test_tools_somatic_modules.config' }
-}
-
 // Function to ensure that resource requirements don't go beyond
 // a maximum limit
 def check_max(obj, type) {