nf-core_sarek/.travis.yml at cd552e847c314fd7216810113a6607aeafee19c6 · maxulysse/nf-core_sarek · GitHub

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sudo: required

language: java

jdk: openjdk8

node_js: "node"

services:
  - docker

env:
  - NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=TOOLS TOOL_INSTALL=all
  - NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=MANTA TOOL_INSTALL=all
  - NXF_VER=0.27.0 PROFILE=docker TEST=MANTA TOOL_INSTALL=nextflow
  - NXF_VER=0.27.0 PROFILE=docker TEST=TOOLS TOOL_INSTALL=nextflow
  - NXF_VER=0.27.0 PROFILE=docker TEST=ANNOTATEVEP TOOL_INSTALL=nextflow
  - NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=ANNOTATESNPEFF TOOL_INSTALL=all
  - NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=STEP TOOL_INSTALL=all
  - NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=GERMLINE TOOL_INSTALL=all
  - NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=DIR TOOL_INSTALL=all
  - NXF_VER=0.27.0 PROFILE=docker TEST=ANNOTATESNPEFF TOOL_INSTALL=nextflow
  - NXF_VER=0.27.0 PROFILE=docker TEST=STEP TOOL_INSTALL=nextflow
  - NXF_VER=0.27.0 PROFILE=docker TEST=GERMLINE TOOL_INSTALL=nextflow
  - NXF_VER=0.27.0 PROFILE=docker TEST=DIR TOOL_INSTALL=nextflow

install: # Install Nextflow (and Singularity if needed)
  - "./scripts/install.sh --tool $TOOL_INSTALL"
  - "travis_retry ./scripts/containers.sh --profile $PROFILE --test $TEST"
  - "npm install -g gnomon"

before_script: # Build references when needed
  - "./scripts/test.sh --profile $PROFILE --test $TEST --build | gnomon --medium 120.0 --high 600.0 --real-time=false"

script:
  - "./scripts/test.sh --profile $PROFILE --test $TEST | gnomon --medium 120.0 --high 600.0 --real-time=false"