.gitlab-ci.yml

# This file is a template, and might need editing before it works on your project.
# see https://docs.gitlab.com/ce/ci/yaml/README.html for all available options

# you can delete this line if you're not using Docker
image: busybox:latest

before_script:
  - echo "Creating cellranger test install"
#  - mkdir -p ~/local/lib/bin
#  - if [[ -w ~/local/lib/bin ]]; then echo "install directory writeable"; else echo "install directory not writeable"; fi
#  - cd ~/local/lib/bin
#  - echo "Downloading cellranger"
#  - wget -O cellranger-3.1.0.tar.gz "http://cf.10xgenomics.com/releases/cell-exp/cellranger-3.1.0.tar.gz?Expires=1564080778&Policy=eyJTdGF0ZW1lbnQiOlt7IlJlc291cmNlIjoiaHR0cDovL2NmLjEweGdlbm9taWNzLmNvbS9yZWxlYXNlcy9jZWxsLWV4cC9jZWxscmFuZ2VyLTMuMS4wLnRhci5neiIsIkNvbmRpdGlvbiI6eyJEYXRlTGVzc1RoYW4iOnsiQVdTOkVwb2NoVGltZSI6MTU2NDA4MDc3OH19fV19&Signature=m6fJx3etqOoywnpHgADfRzpCSZ04YZEe0sA3ZyVl1EQMn5Zm60qLk7v4KVPRLy6a9Qi2zE5DKWr8EpFfAg3kWqZ5-vDYtZtlYAnl0~OhtijIyYs7Rm8Uqzal-lk8tmD4SQaZQVQY~RLEed7iWq7stYwc4QTXRUjtojGqwMvqf5t4dMQbn7tNs513shjC4lGfL7~xCWpc5vaxaSN9wGSRF8ex9Hy-GsMYG2Dm8ya7ajplR1SPqTcHd9sDfro1UzOK~IGkHh9GGO9EicXQ6ypExvKB-WrDLLLZ66rEJjeNoSS6qnTKeEzyKw-3UoEYfho~Ph4eKrFS-XSZhtEX-UDItg__&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA"
#  - tar -xzvf cellranger-3.1.0.tar.gz
#  - echo "Downloading reference for human genome"
#  - wget http://cf.10xgenomics.com/supp/cell-exp/refdata-cellranger-GRCh38-3.0.0.tar.gz
#  - tar -xzvf refdata-cellranger-GRCh38-3.0.0.tar.gz
  - echo "cellranger added to PATH"
  - export PATH=/home/tom/local/lib/bin/cellranger-3.1.0:$PATH
  - cellranger --version
  - cellranger testrun --id "test"
  - cd -
  
after_script:
  - echo "Testing complete"
   
build1:
  stage: build
  script:
    - echo "testing script call"
    - bash convert.sh --version
    - bash convert.sh --help
    - echo "testing setup"
    - bash convert.sh --technology "Nadia" --setup
    - bash convert.sh --technology "10x" --setup
    - bash convert.sh --technology "iCELL8" --setup
    - echo "conversion script configured and able to write to barcodes"
   
test1:
  stage: test
  script: convert.sh
    - echo "test 10x"
    - bash convert.sh -t "10x" -r "~/home/local/lib/cellranger-3.1.0/cellranger-tiny-ref/3.0.0" \
    - --read1 "~/home/local/lib/cellranger-3.1.0/cellranger-tiny-ref/3.0.0/tinygex_S1_L001_R1_001.fastq.gz" \
    - --read2 "~/home/local/lib/cellranger-3.1.0/cellranger-tiny-ref/3.0.0/tinygex_S1_L001_R2_001.fastq.gz"
    - echo "test Nadia"
    - bash convert.sh -t "Nadia" -r "~/home/local/lib/cellranger-3.1.0/cellranger-tiny-ref/3.0.0" \
    - --read1 "~/home/local/lib/cellranger-3.1.0/cellranger-tiny-ref/3.0.0/tinygex_S1_L001_R1_001.fastq.gz" \
    - --read2 "~/home/local/lib/cellranger-3.1.0/cellranger-tiny-ref/3.0.0/tinygex_S1_L001_R2_001.fastq.gz"
    - echo "test iCELL8"
    - bash convert.sh -t "Nadia" -r "~/home/local/lib/cellranger-3.1.0/cellranger-tiny-ref/3.0.0" \
    - --read1 "~/home/local/lib/cellranger-3.1.0/cellranger-tiny-ref/3.0.0/tinygex_S1_L001_R1_001.fastq.gz" \
    - --read2 "~/home/local/lib/cellranger-3.1.0/cellranger-tiny-ref/3.0.0/tinygex_S1_L001_R2_001.fastq.gz"
   
test2:
  stage: test 
  script: convert.sh
    - echo "test file inputs"
    - bash convert.sh -t "icell8" -r "~/home/local/lib/cellranger-3.1.0/cellranger-tiny-ref/3.0.0" \
    - -- file "~/home/local/lib/cellranger-3.1.0/cellranger-tiny-ref/3.0.0/tinygex_S1_L001" 
    - echo "test multiple lanes"
    - bash convert.sh -t "Nadia" -r "~/home/local/lib/cellranger-3.1.0/cellranger-tiny-ref/3.0.0" \
    - --read1 "~/home/local/lib/cellranger-3.1.0/cellranger-tiny-ref/3.0.0/tinygex_S1_L001_R1_001.fastq.gz" \
    - --read1 "~/home/local/lib/cellranger-3.1.0/cellranger-tiny-ref/3.0.0/tinygex_S1_L002_R1_001.fastq.gz" \
    - "~/home/local/lib/cellranger-3.1.0/cellranger-tiny-ref/3.0.0/tinygex_S1_L001_R2_001.fastq.gz"\
    - "~/home/local/lib/cellranger-3.1.0/cellranger-tiny-ref/3.0.0/tinygex_S1_L002_R2_001.fastq.gz"
    - echo "test file inputs"
    - bash convert.sh -t "icell8" -r "~/home/local/lib/cellranger-3.1.0/cellranger-tiny-ref/3.0.0" \
    - --file "~/home/local/lib/cellranger-3.1.0/cellranger-tiny-ref/3.0.0/tinygex_S1_L001" \
    - "~/home/local/lib/cellranger-3.1.0/cellranger-tiny-ref/3.0.0/tinygex_S1_L002"

   
deploy1:
  stage: deploy
  script:
    - echo "Checks completed"