From c8f728a7bf1af6d71737b96d256e3ee92699cffd Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 15 Sep 2022 12:08:00 +0200
Subject: [PATCH] remove file

---
 conf/test_tools_somatic_modules.config | 45 --------------------------
 1 file changed, 45 deletions(-)
 delete mode 100644 conf/test_tools_somatic_modules.config

diff --git a/conf/test_tools_somatic_modules.config b/conf/test_tools_somatic_modules.config
deleted file mode 100644
index 4a44b3e34d..0000000000
--- a/conf/test_tools_somatic_modules.config
+++ /dev/null
@@ -1,45 +0,0 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Nextflow config file for running minimal tests
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Extra DSL2 module specific options for CI tests
-    To be loaded after the modules.config files
-    To be used with the tools_somatic(_ascat).config files
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-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" }
-    }
-}