diff --git a/.travis.yml b/.travis.yml
index 2958db8..2b37dd4 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -26,4 +26,4 @@ env:
 
 script:
   # Run the pipeline with the test profile and test remote config
-  - nextflow run nf-core/hlatyping -r dev --custom_config_base ${TRAVIS_BUILD_DIR} -profile test_configs,test,docker
+  - nextflow run ${TRAVIS_BUILD_DIR}/configtest.nf -profile
diff --git a/conf/test_configs.config b/conf/test_configs.config
deleted file mode 100644
index 7c6c340..0000000
--- a/conf/test_configs.config
+++ /dev/null
@@ -1 +0,0 @@
-// Empty config for integration test purposes.
\ No newline at end of file
diff --git a/nfcore_custom.config b/nfcore_custom.config
index 8390b23..dfcb4d2 100644
--- a/nfcore_custom.config
+++ b/nfcore_custom.config
@@ -22,7 +22,6 @@ profiles {
   munin        { includeConfig "${params.custom_config_base}/conf/munin.config" }
   phoenix      { includeConfig "${params.custom_config_base}/conf/phoenix.config" }
   shh          { includeConfig "${params.custom_config_base}/conf/shh.config" }
-  test_configs { includeConfig "${params.custom_config_base}/conf/test_configs.config"}
   uct_hex      { includeConfig "${params.custom_config_base}/conf/uct_hex.config" }
   uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config"
                  includeConfig "${params.custom_config_base}/conf/uppmax-devel.config"