.gitlab-ci.yml

before_script:
  - module add  python/3.6.4-anaconda
  - pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1
  - module load singularity/3.0.2
  - module load nextflow/19.09.0
  - ln -sfn /project/BICF/BICF_Core/shared/gudmap/test_data/* ./test_data/
  - mkdir -p ~/.deriva
  - mkdir -p ~/.bdbag

stages:
  - unit
  - integration

getBag:
  stage: unit
  script:
  - ln -sfn `readlink -e ./test_data/auth/credential.json` ~/.deriva/credential.json
  - singularity run 'docker://bicf/gudmaprbkfilexfer:1.3' deriva-download-cli dev.gudmap.org --catalog 2 ./workflow/conf/replicate_export_config.json . rid=16-1ZX4
  - pytest -m getBag

getData:
  stage: unit
  script:
  - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
  - unzip ./test_data/bagit/Study_Q-Y4H0.zip
  - singularity run 'docker://bicf/gudmaprbkfilexfer:1.3' bash ./workflow/scripts/bdbagFetch.sh Study_Q-Y4H0 Q-Y4H0 TEST
  - pytest -m getData

parseMetadata:
  stage: unit
  script:
  - singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p repRID
  - singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p ends
  - singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsManual
  - singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p stranded
  - singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p species

inferMetadata:
  stage: unit
  script:
  - >
    align=$(echo $(grep "Overall alignment rate" ./test_data/meta/Q-Y5JA_1M.se.alignSummary.txt | cut -f2 -d ':' | cut -f2 -d ' ' | tr -d '%'))
    if [[ ${align} == "" ]]
    then
      exit 1
    fi
  - >
    singularity run 'docker://bicf/rseqc3.0:2.0.0' infer_experiment.py -r "/project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed" -i "./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam" 1>> Q-Y5JA_1M.se.inferMetadata.log
    ended=`bash inferMeta.sh endness Q-Y5JA_1M.se.inferMetadata.log
    if [[ ${ended} == "" ]]
    then
      exit 1
    fi
  - pytest -m inferMetadata

getRef:
  stage: unit
  script:
  - mkdir -p hu
  - mkdir -p mo
  - cp -R /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2 ./hu/
  - cp -R /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2 ./mo/

trimData:
  stage: unit
  script:
  - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --basename Q-Y5JA_1M.se -j 20 ./test_data/fastq/small/Q-Y5JA_1M.R1.fastq.gz
  - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --paired --basename Q-Y5JA_1M.pe -j 20 ./test_data/fastq/small/Q-Y5JA_1M.R1.fastq.gz ./test_data/fastq/small/Q-Y5JA_1M.R2.fastq.gz
  - pytest -m trimData