.gitlab-ci.yml

before_script:
  - module add  python/3.6.1-2-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/Replicate_16-1ZX4
  - singularity run 'docker://bicf/gudmaprbkfilexfer:1.3' sh ./workflow/scripts/bdbagFetch.sh Replicate_16-1ZX4 16-1ZX4
  - 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 specie

trimData:
  stage: unit
  script:
  - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --basename 16-1ZX4 -j `nproc` ./test_data/fastq/16-1ZX4.R1.fastq.gz
  - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --paired --basename Q-Y5JA -j `nproc` ./test_data/fastq/Q-Y5JA.R1.fastq.gz ./test_data/fastq/Q-Y5JA.R2.fastq.gz
  - pytest -m trimData

alignReads:
  stage: unit
  script:
  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz Q-Y5JA.unal.gz -S Q-Y5JA.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12/hisat2/genome --rna-strandness FR --no-mixed --no-discordant -1 ./test_data/fastq/Q-Y5JA_R1_val_1.fq.gz -2 ./test_data/fastq/Q-Y5JA_R2_val_2.fq.gz
  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o Q-Y5JA.bam Q-Y5JA.sam
  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ `nproc` -O BAM -o Q-Y5JA.sorted.bam Q-Y5JA.bam
  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b Q-Y5JA.sorted.bam Q-Y5JA.sorted.bai
  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz 16-1ZX4.unal.gz -S 16-1ZX4.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12/hisat2/genome --rna-strandness FR -U ./test_data/fastq/16-1ZX4_trimmed.fq.gz
  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o 16-1ZX4.bam 16-1ZX4.sam
  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ `nproc` -O BAM -o 16-1ZX4.sorted.bam 16-1ZX4.bam
  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b 16-1ZX4.sorted.bam 16-1ZX4.sorted.bai
  - pytest -m alignData

dedupReads:
  stage: unit
  script:
  - singularity run 'docker://bicf/picard2.21.7:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=${sortedBam} O=${repRID}.deduped.bam M=${repRID}.deduped.Metrics.txt REMOVE_DUPLICATES=true
  - pytest -m dedupData

integration_se:
  stage: integration
  script:
  - nextflow run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-1ZX4

integration_pe:
  stage: integration