Adds profile integration tests

.travis.yml

@@ -0,0 +1,28 @@
+sudo: required
+language: python
+jdk: openjdk8
+services:
+  - docker
+python:
+  - '3.6'
+cache: pip
+matrix:
+  fast_finish: true
+
+before_install:
+  # PRs to master are only ok if coming from dev branch
+  - '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && [ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ])'
+
+install:
+  # Install Nextflow
+  - mkdir /tmp/nextflow && cd /tmp/nextflow
+  - wget -qO- get.nextflow.io | bash
+  - sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
+
+env:
+  - NXF_VER='18.10.1' # Specify a minimum NF version that should be tested and work
+  - NXF_VER='' # Plus: get the latest NF version and check, that it works
+
+script:
+  # Run the pipeline with the test profile and test remote config
+  - nextflow run nf-core/hlatyping -profile test_configs,test,docker

conf/test_configs.config

@@ -0,0 +1 @@
+// Empty config for integration test purposes.

nfcore_custom.config

@@ -22,6 +22,7 @@ profiles {
   munin        { includeConfig "${params.custom_config_base}/munin.config" }
   phoenix      { includeConfig "${params.custom_config_base}/phoenix.config" }
   shh          { includeConfig "${params.custom_config_base}/shh.config" }
+  test_configs { includeConfig "${params.custom_config_base}/test_configs.config"}
   uct_hex      { includeConfig "${params.custom_config_base}/uct_hex.config" }
   uppmax_devel { includeConfig "${params.custom_config_base}/uppmax.config"
                  includeConfig "${params.custom_config_base}/uppmax-devel.config"