Merge pull request #24 from nf-core/dev

Include config integration test

.travis.yml

@@ -0,0 +1,29 @@
+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
+  - mkdir -p ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
+
+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
+  - grep "{.*includeConfig.*[a-z]*\.config\"" ${TRAVIS_BUILD_DIR}/nfcore_custom.config | tr -s ' ' | cut -d " " -f 2 | xargs -I {} nextflow run ${TRAVIS_BUILD_DIR}/configtest.nf -profile {}

configtest.nf

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+#!/usr/bin/env nextflow
+
+def separator = "-"*40
+print("$separator\n")
+print("Parameter scope for config \'${workflow.profile}\'\n")
+print("$separator\n")
+params.each {
+    assert it
+    print("\t$it\n")
+}

nextflow.config

@@ -0,0 +1 @@
+includeConfig("nfcore_custom.config")