eager/.travis.yml at b9d61731ba2244259380cfd8531bfbda670e589d · maxibor/eager · GitHub

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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" ])'
  # Pull the docker image first so the test doesn't wait for this
  - docker pull nfcore/eager:dev
  # Fake the tag locally so that the pipeline runs properly
  # Looks weird when this is :dev to :dev, but makes sense when testing code for a release (:dev to :1.0.1)
  - docker tag nfcore/eager:dev nfcore/eager: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
  # Install nf-core/tools
  - pip install --upgrade pip
  - pip install nf-core
  # Install Conda
  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
  - bash Miniconda3-latest-Linux-x86_64.sh -b -f -p $HOME/miniconda
  - export PATH="$HOME/miniconda/bin:$PATH"
  # Reset
  - mkdir ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
  # Install markdownlint-cli
  - sudo apt-get install npm && npm install -g markdownlint-cli

env:
  - NXF_VER='0.32.0' # 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:
  # Lint the pipeline code
  - nf-core lint ${TRAVIS_BUILD_DIR}
  # Run the basic pipeline with the test profile
  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --saveReference
  # Run the basic pipeline with single end data (pretending its single end actually)
  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --singleEnd --bwa_index results/reference_genome/bwa_index/bwa_index/
  # Run the basic pipeline with paired end data without collapsing
  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --skip_collapse --saveReference
  # Run the basic pipeline with paired end data without trimming
  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --skip_trim --saveReference
   # Run the basic pipeline with paired end data without adapterRemoval
  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --skip_adapterremoval --saveReference
   # Run the basic pipeline with output unmapped reads as fastq
  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --strip_input_fastq
  # Run the same pipeline testing optional step: fastp, complexity
  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --complexity_filter --bwa_index results/reference_genome/bwa_index/bwa_index/
  # Test BAM Trimming
  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --trim_bam --bwa_index results/reference_genome/bwa_index/bwa_index/
  # Test running with CircularMapper
  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --circularmapper --circulartarget 'NC_007596.2'
  # Test running with BWA Mem
  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --bwamem --bwa_index results/reference_genome/bwa_index/bwa_index/
  # Test with zipped reference input
  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --fasta 'https://raw.githubusercontent.com/nf-core/test-datasets/eager2/reference/Test.fasta.gz'
  # Run the basic pipeline with the bam input profile
  - nextflow run ${TRAVIS_BUILD_DIR} -profile testbam,docker --bam