.gitlab-ci.yml

before_script:
  - module load python/3.6.4-anaconda
  - pip install --user attrs==20.3.0 pytest==6.2.2 pytest-pythonpath==0.7.3 pytest-cov==2.11.1
  - module load singularity/3.5.3
  - export SINGULARITY_CACHEDIR=${dir}cache/
  - module load nextflow/20.01.0
  - ln -sfn /project/BICF/BICF_Core/shared/gudmap/test_data/* ./test_data/
  - mkdir -p ~/.deriva
  - mkdir -p ~/.bdbag

after_script:
  - unset SINGULARITY_CACHEDIR

variables:
  refMoVersion: "38.p6.vM25"
  refHuVersion: "38.p13.v36"
  refERCCVersion: "92"
  dir: "/project/BICF/BICF_Core/shared/gudmap/singularity_cache/"

stages:
  - environment
  - singularity
  - versions
  - aggregation
  - badges
  - deploy
  - unit
  - reference
  - integration
  - consistency


img_cache:
  stage: singularity
  script:
    - mkdir -p ${dir}cache/
    - cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | xargs -P 1 -I {} bash -c "singularity pull --dir ${dir} 'docker://'{} || true"
    - wait
    - echo images cached

collect:
  stage: versions
  script:
    - derivaImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deriva | cut -d"/" -f2 | cut -d":" -f1)
    - derivaVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deriva | cut -d"/" -f2 | cut -d":" -f2)
    - echo ${dir}${derivaImg}_${derivaVar}.sif
    - singularity run ${dir}${derivaImg}_${derivaVar}.sif deriva-download-cli --version > version_deriva.txt
    - singularity run ${dir}${derivaImg}_${derivaVar}.sif bdbag --version > version_bdbag.txt
    - pythonImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep python | cut -d"/" -f2 | cut -d":" -f1)
    - pythonVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep python | cut -d"/" -f2 | cut -d":" -f2)
    - echo ${dir}${pythonImg}_${pythonVar}.sif
    - singularity run ${dir}${pythonImg}_${pythonVar}.sif python3 --version > version_python.txt
    - fastqcImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep fastqc | cut -d"/" -f2 | cut -d":" -f1)
    - fastqcVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep fastqc | cut -d"/" -f2 | cut -d":" -f2)
    - echo ${dir}${fastqcImg}_${fastqcVar}.sif
    - singularity run ${dir}${fastqcImg}_${fastqcVar}.sif fastqc --version > version_fastqc.txt
    - seqwhoImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqwho | cut -d"/" -f2 | cut -d":" -f1)
    - seqwhoVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqwho | cut -d"/" -f2 | cut -d":" -f2)
    - echo ${dir}${seqwhoImg}_${seqwhoVar}.sif
    - singularity run ${dir}${seqwhoImg}_${seqwhoVar}.sif seqwho.py -h | grep -o Version.* > version_seqwho.txt &
    - trimgaloreImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep trimgalore | cut -d"/" -f2 | cut -d":" -f1)
    - trimgaloreVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep trimgalore | cut -d"/" -f2 | cut -d":" -f2)
    - echo ${dir}${trimgaloreImg}_${trimgaloreVar}.sif
    - singularity run ${dir}${trimgaloreImg}_${trimgaloreVar}.sif trim_galore --version > version_trimgalore.txt
    - seqtkImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqtk | cut -d"/" -f2 | cut -d":" -f1)
    - seqtkVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqtk | cut -d"/" -f2 | cut -d":" -f2)
    - echo ${dir}${seqtkImg}_${seqtkVar}.sif
    - singularity run ${dir}${seqtkImg}_${seqtkVar}.sif seqtk 2>&1 | grep -o Version.* > version_seqtk.txt &
    - rseqcImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep rseqc | cut -d"/" -f2 | cut -d":" -f1)
    - rseqcVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep rseqc | cut -d"/" -f2 | cut -d":" -f2)